Difference between revisions of "2022 AMS-535 Fall"

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=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage </center> ===
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=== <center> Please see https://ringo.ams.stonybrook.edu/~rizzo for Rizzo Group Homepage </center> ===
 
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{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"
 
{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"
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*The bulk of the classes will be devoted to Discussion of papers read prior to coming to class (2 per class) for which everyone will also have watched oral presentations prior to coming to class (2 per class). Oral presentations will be in the form of pre-recorded videos made by students taking the class.  
 
*The bulk of the classes will be devoted to Discussion of papers read prior to coming to class (2 per class) for which everyone will also have watched oral presentations prior to coming to class (2 per class). Oral presentations will be in the form of pre-recorded videos made by students taking the class.  
 
*During the Discussion sessions which are held in person the Instructors(s) will ask participants to explain details of the papers they have read which will form the basis of the "Discussion/Participation" part of their grade. Thus, it is important that everyone attend all of the classes. All students are expected to participate especially those whose papers are being discussed that day. As noted above each student will prepare two questions per paper to facilitate discussion.  Your questions, and any answers that may have been discussed in class, will be uploaded into Google Forms (details to be given in class) by midnight of the day the papers are covered.   
 
*During the Discussion sessions which are held in person the Instructors(s) will ask participants to explain details of the papers they have read which will form the basis of the "Discussion/Participation" part of their grade. Thus, it is important that everyone attend all of the classes. All students are expected to participate especially those whose papers are being discussed that day. As noted above each student will prepare two questions per paper to facilitate discussion.  Your questions, and any answers that may have been discussed in class, will be uploaded into Google Forms (details to be given in class) by midnight of the day the papers are covered.   
*If a student is unable to attend a specific class for reasons beyond their control they will instead be asked to email the instructor(s) AND submit a one page  [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.paper.summary.docx Paper Summary Sheet] answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Discussion" part of their grade for any synchronous classes that were missed.
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*If a student is unable to attend a specific class for reasons beyond their control they will instead be asked to email the instructor(s) AND submit a one page  [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.paper.summary.docx Paper Summary Sheet] answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Discussion" part of their grade for any synchronous classes that were missed.
 
*If a students misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted.  
 
*If a students misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted.  
 
*Please note that this is an in-person class and all participants are expected to attend each and every class.
 
*Please note that this is an in-person class and all participants are expected to attend each and every class.
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*Students will email their pre-recorded presentations to ALL course Instructors by Friday at 5PM before the week in which their presentations will be discussed.  
 
*Students will email their pre-recorded presentations to ALL course Instructors by Friday at 5PM before the week in which their presentations will be discussed.  
 
*Course participants will watch the student presentations before the class in which they are to be discussed.
 
*Course participants will watch the student presentations before the class in which they are to be discussed.
*Course participants will score each student presentation using a [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.presentation.assessment.docx Presentation Assessment Sheet] which will be emailed to ALL Instructors within 24 hours after the class in which the presentation were discussed.
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*Course participants will score each student presentation using a [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.presentation.assessment.docx Presentation Assessment Sheet] which will be emailed to ALL Instructors within 24 hours after the class in which the presentation were discussed.
  
 
'''Take home Quizzes:'''
 
'''Take home Quizzes:'''
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*''Organizational Meeting
 
*''Organizational Meeting
||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.22.ams535.rizzo.organizational.mp4 Rizzo, R. mp4]
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||[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.22.ams535.rizzo.organizational.mp4 Rizzo, R. mp4]
 
|| Course introduction and format.  Go over Syllabus.  Course participant background and introductions.
 
|| Course introduction and format.  Go over Syllabus.  Course participant background and introductions.
 
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.mp4 Rizzo, R. mp4]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.mp4 Rizzo, R. mp4]
 
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.pdf Rizzo, R. pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.pdf Rizzo, R. pdf]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen009.pdf Jorgensen, W.L., The many roles of computation in drug discovery. ''Science'' '''2004''', ''303'', 1813-8]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen009.pdf Jorgensen, W.L., The many roles of computation in drug discovery. ''Science'' '''2004''', ''303'', 1813-8]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz004.pdf Kuntz, I. D., Structure-based strategies for drug design and discovery. ''Science'' '''1992''', ''257'', 1078-1082]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz004.pdf Kuntz, I. D., Structure-based strategies for drug design and discovery. ''Science'' '''1992''', ''257'', 1078-1082]
 
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.mp4 Rizzo, R. mp4]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.mp4 Rizzo, R. mp4]
 
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<br>
 
<br>
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.pdf Rizzo, R. pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.pdf Rizzo, R. pdf]
 
|| <center>in class lecture</center>
 
|| <center>in class lecture</center>
 
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.mp4 Rizzo, R. mp4]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.mp4 Rizzo, R. mp4]
 
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<br>
 
<br>
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.pdf Rizzo, R. pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.pdf Rizzo, R. pdf]
 
|| <center>in class lecture</center>
 
|| <center>in class lecture</center>
|| [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/2010.amino_acids_scanned.pdf structures of the 20 amino acid side chains]
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|| [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/2010.amino_acids_scanned.pdf structures of the 20 amino acid side chains]
 
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:2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive   
 
:2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive   
 
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.mp4 Rizzo, R. mp4]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.mp4 Rizzo, R. mp4]
 
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<br>
 
<br>
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.pdf Rizzo, R. pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.pdf Rizzo, R. pdf]
 
|| <center>in class lecture</center>
 
|| <center>in class lecture</center>
 
|| <center>-</center>
 
|| <center>-</center>
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:2. Structure Quality, PDB in detail  
 
:2. Structure Quality, PDB in detail  
 
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.mp4 Rizzo, R. mp4]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.mp4 Rizzo, R. mp4]
 
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<br>
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.pdf Rizzo, R. pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.pdf Rizzo, R. pdf]
 
|| <center>in class lecture</center>
 
|| <center>in class lecture</center>
 
|| <center>-</center>
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.mp4 Outhwaite, Ian mp4]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.mp4 Outhwaite, Ian mp4]
 
<br>
 
<br>
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.pdf  pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk01.pdf  pdf]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.mp4 Marr, Douglas mp4]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.mp4 Marr, Douglas mp4]
 
<br>
 
<br>
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.pdf  pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.14.AMS535.talk02.pdf  pdf]
  
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Mackerell001.pdf Mackerell, A. D., Jr., Empirical force fields for biological macromolecules: overview and issues. ''J. Comput. Chem.'' '''2004''', ''25'', 1584-604]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Mackerell001.pdf Mackerell, A. D., Jr., Empirical force fields for biological macromolecules: overview and issues. ''J. Comput. Chem.'' '''2004''', ''25'', 1584-604]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen002.pdf Jorgensen, W. L.; et al., Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. ''J. Am. Chem. Soc.'' '''1996''', ''118'', 11225-11236]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen002.pdf Jorgensen, W. L.; et al., Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. ''J. Am. Chem. Soc.'' '''1996''', ''118'', 11225-11236]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/vangunsteren003.pdf van Gunsteren, W. F.; et al., Biomolecular modeling: Goals, problems, perspectives. ''Angew. Chem. Int. Ed. Engl.'' '''2006''', ''45'', 4064-92]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/vangunsteren003.pdf van Gunsteren, W. F.; et al., Biomolecular modeling: Goals, problems, perspectives. ''Angew. Chem. Int. Ed. Engl.'' '''2006''', ''45'', 4064-92]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen004.pdf Jorgensen, W. L.; et al., The Opls Potential Functions For Proteins - Energy Minimizations For Crystals of Cyclic-Peptides and Crambin. ''J. Am. Chem. Soc.'' '''1988''', ''110'', 1657-1671]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen004.pdf Jorgensen, W. L.; et al., The Opls Potential Functions For Proteins - Energy Minimizations For Crystals of Cyclic-Peptides and Crambin. ''J. Am. Chem. Soc.'' '''1988''', ''110'', 1657-1671]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.mp4 Li, Stan mp4]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.mp4 Li, Stan mp4]
 
<br>
 
<br>
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.pdf  pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk01.pdf  pdf]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.mp4 Dar, Nauroz mp4]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.mp4 Dar, Nauroz mp4]
 
<br>
 
<br>
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.pdf  pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.19.AMS535.talk02.pdf  pdf]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman004.pdf Cornell, W. D.; et al., A Second Generation Force Field For the Simulation of Proteins, Nucleic Acids, and Organic Molecules. ''J. Am. Chem. Soc.'' '''1995''', ''117'', 5179-5197]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman004.pdf Cornell, W. D.; et al., A Second Generation Force Field For the Simulation of Proteins, Nucleic Acids, and Organic Molecules. ''J. Am. Chem. Soc.'' '''1995''', ''117'', 5179-5197]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen003.pdf Jorgensen, W. L.; et al., Comparison of Simple Potential Functions for Simulating Liquid Water. ''J. Chem. Phys.'' '''1983''', ''79'', 926-935]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen003.pdf Jorgensen, W. L.; et al., Comparison of Simple Potential Functions for Simulating Liquid Water. ''J. Chem. Phys.'' '''1983''', ''79'', 926-935]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman005.pdf Bayly, C. I.; et al., A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints For Deriving Atomic Charges - the RESP Model. ''J. Phys. Chem.'' '''1993''', ''97'', 10269-10280]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman005.pdf Bayly, C. I.; et al., A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints For Deriving Atomic Charges - the RESP Model. ''J. Phys. Chem.'' '''1993''', ''97'', 10269-10280]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.mp4  Mannaf, Aniqa mp4]  
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.mp4  Mannaf, Aniqa mp4]  
 
<br>
 
<br>
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.pdf  pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk01.pdf  pdf]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.mp4  Biju, Bismi mp4]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.mp4  Biju, Bismi mp4]
 
<br>
 
<br>
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.pdf  pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.21.AMS535.talk02.pdf  pdf]
  
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen010.pdf Jorgensen, W. L.;  et al., Monte Carlo Simulation of Differences in Free Energies of Hydration. ''J. Chem. Phys.'' '''1985''', ''83'', 3050-3054]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen010.pdf Jorgensen, W. L.;  et al., Monte Carlo Simulation of Differences in Free Energies of Hydration. ''J. Chem. Phys.'' '''1985''', ''83'', 3050-3054]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Still001.pdf Still, W. C.; et al., Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. ''J. Am. Chem. Soc'' 1990, ''112'', 6127-6129]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Still001.pdf Still, W. C.; et al., Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. ''J. Am. Chem. Soc'' 1990, ''112'', 6127-6129]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/DDGhyd_cycle.pdf Thermodynamic Cycle as Drawn By Dr. Rizzo]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/DDGhyd_cycle.pdf Thermodynamic Cycle as Drawn By Dr. Rizzo]
  
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.mp4  Kakade, Yogesh mp4]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.mp4  Kakade, Yogesh mp4]
 
<br>
 
<br>
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.pdf  pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk01.pdf  pdf]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.mp4  Becker, Kindra mp4]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.mp4  Becker, Kindra mp4]
 
<br>
 
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.pdf  pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.26.AMS535.talk02.pdf  pdf]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Honig001.pdf Sitkoff, D.; et al., Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. ''J. Phys. Chem.'' '''1994''', ''98'', 1978-1988]  
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Honig001.pdf Sitkoff, D.; et al., Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. ''J. Phys. Chem.'' '''1994''', ''98'', 1978-1988]  
  
2.  [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo011.pdf Rizzo, R. C.; et al., Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. ''J. Chem. Theory. Comput.'' '''2006''', ''2'', 128-139]
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2.  [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo011.pdf Rizzo, R. C.; et al., Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. ''J. Chem. Theory. Comput.'' '''2006''', ''2'', 128-139]
 
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||<center>'''Take home QUIZ for Section 2 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center>
 
||<center>'''Take home QUIZ for Section 2 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center>
 
||<center>'''Additional resources:'''</center>
 
||<center>'''Additional resources:'''</center>
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Duarte01.pdf Duarte Ramos Matos, G.; et al., Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database. ''J. Chem. Eng. Data'' '''2017''', ''62'', 1559-1569] <br>  
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Duarte01.pdf Duarte Ramos Matos, G.; et al., Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database. ''J. Chem. Eng. Data'' '''2017''', ''62'', 1559-1569] <br>  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Loeffler01.pdf Loeffler, H. H.; et al., Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages ''J. Chem. Theory Comput.'' '''2018''', ''14'', 5567−5582]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Loeffler01.pdf Loeffler, H. H.; et al., Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages ''J. Chem. Theory Comput.'' '''2018''', ''14'', 5567−5582]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.mp4  Snyders, Hayden mp4]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.mp4  Snyders, Hayden mp4]
 
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.pdf  pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk01.pdf  pdf]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.mp4 Cheung, Andrew mp4]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.mp4 Cheung, Andrew mp4]
 
<br>
 
<br>
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.pdf  pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.28.AMS535.talk02.pdf  pdf]
  
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman011.pdf Howard, A. E.; Kollman, P. A., An analysis of current methodologies for conformational searching of complex molecules. ''J. Med. Chem.'' '''1988''', ''31'', 1669-75]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman011.pdf Howard, A. E.; Kollman, P. A., An analysis of current methodologies for conformational searching of complex molecules. ''J. Med. Chem.'' '''1988''', ''31'', 1669-75]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Petsko001.pdf Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. ''Nature'' '''1990''', ''347'', 631-9]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Petsko001.pdf Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. ''Nature'' '''1990''', ''347'', 631-9]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Colby_College_MMtutor.pdf Section 4 (PAGES 22-27) Colby College Molecular Mechanics Tutorial Introduction, 2004, Shattuck, T.W., Colby College]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Colby_College_MMtutor.pdf Section 4 (PAGES 22-27) Colby College Molecular Mechanics Tutorial Introduction, 2004, Shattuck, T.W., Colby College]
  
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Holloway001.pdf Holloway, M. K., A priori prediction of ligand affinity by energy minimization. ''Perspect. Drug Discov. Design'' '''1998''', ''9-11'', 63-84]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Holloway001.pdf Holloway, M. K., A priori prediction of ligand affinity by energy minimization. ''Perspect. Drug Discov. Design'' '''1998''', ''9-11'', 63-84]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.mp4 Cordero, Ricardo mp4]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.mp4 Cordero, Ricardo mp4]
 
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.pdf  pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk01.pdf  pdf]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.mp4 Chong, Jiyun mp4]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.mp4 Chong, Jiyun mp4]
 
<br>
 
<br>
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.pdf  pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.03.AMS535.talk02.pdf  pdf]
  
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Luke001.pdf Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B.]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Luke001.pdf Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B.]
  
1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen007.pdf Jorgensen, W. L.; TiradoRives, J., Monte Carlo vs Molecular Dynamics for Conformational Sampling. ''J. Phys. Chem.'' '''1996''', ''100'',14508-14513]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen007.pdf Jorgensen, W. L.; TiradoRives, J., Monte Carlo vs Molecular Dynamics for Conformational Sampling. ''J. Phys. Chem.'' '''1996''', ''100'',14508-14513]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill001.pdf Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. ''Nat. Struct. Biol.'' '''1997''', ''4'', 10-19]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill001.pdf Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. ''Nat. Struct. Biol.'' '''1997''', ''4'', 10-19]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Metropolis001.pdf Metropolis, N.;et al., Equation of State Calculations by Fast Computing Machines. ''The Journal of Chemical Physics'' '''1953''', ''21'', 1087-1092]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Metropolis001.pdf Metropolis, N.;et al., Equation of State Calculations by Fast Computing Machines. ''The Journal of Chemical Physics'' '''1953''', ''21'', 1087-1092]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.mp4  Ventura, Carlos mp4]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.mp4  Ventura, Carlos mp4]
 
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.pdf  pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk01.pdf  pdf]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.mp4  Dharmajeewa, Oshini mp4]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.mp4  Dharmajeewa, Oshini mp4]
 
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.pdf  pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.05.AMS535.talk02.pdf  pdf]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Simmerling002.pdf Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. ''J. Am. Chem. Soc.'' '''2002''', ''124'',11258-9]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Simmerling002.pdf Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. ''J. Am. Chem. Soc.'' '''2002''', ''124'',11258-9]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali001.pdf Marti-Renom, M. A.; et al., Comparative protein structure modeling of genes and genomes. ''Annu. Rev. Biophys. Biomol. Struct.'' '''2000''',''29'',291-325]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali001.pdf Marti-Renom, M. A.; et al., Comparative protein structure modeling of genes and genomes. ''Annu. Rev. Biophys. Biomol. Struct.'' '''2000''',''29'',291-325]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Fersht001.pdf Daggett, V.; Fersht, A., The present view of the mechanism of protein folding. ''Nat. Rev. Mol. Cell Biol.'' '''2003''', ''4'', 497-502]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Fersht001.pdf Daggett, V.; Fersht, A., The present view of the mechanism of protein folding. ''Nat. Rev. Mol. Cell Biol.'' '''2003''', ''4'', 497-502]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali002.pdf Fiser, A.; et al., Evolution and physics in comparative protein structure modeling. ''Acc. Chem. Res.'' '''2002''', ''35'', 413-21]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali002.pdf Fiser, A.; et al., Evolution and physics in comparative protein structure modeling. ''Acc. Chem. Res.'' '''2002''', ''35'', 413-21]
 
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.mp4 Moy, Olivia mp4]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.12.AMS535.talk02.mp4 Moy, Olivia mp4]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult002.pdf Moult, J., A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. ''Curr. Opin. Struct. Biol.'' '''2005''',''15'', 285-9]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult002.pdf Moult, J., A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. ''Curr. Opin. Struct. Biol.'' '''2005''',''15'', 285-9]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill002.pdf Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. ''Sci. Adv.'' '''2016''', ''2'']
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill002.pdf Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. ''Sci. Adv.'' '''2016''', ''2'']
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult003.pdf Kryshtafovych, A.; et al., Progress over the first decade of CASP experiments. ''Proteins'' '''2005''', ''61 Suppl 7'', 225-36]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult003.pdf Kryshtafovych, A.; et al., Progress over the first decade of CASP experiments. ''Proteins'' '''2005''', ''61 Suppl 7'', 225-36]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.mp4 Henderson, Max mp4 ]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.mp4 Henderson, Max mp4 ]
 
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.pdf  pdf]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk01.pdf  pdf]
  
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.mp4 Bauer, Jack mp4 ]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.mp4 Bauer, Jack mp4 ]
 
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.pdf  pdf ]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.17.AMS535.talk02.pdf  pdf ]
  
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Amaro001.pdf Durrant, J.;et al, Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ''ACS Central Science'' '''2020''', ''6'', 189-196]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Amaro001.pdf Durrant, J.;et al, Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ''ACS Central Science'' '''2020''', ''6'', 189-196]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Hassabis001.pdf Senior, A.;et al, Improved protein structure prediction using potentials from deep learning. ''Nature'' '''2020''', ''577'', 1-5]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Hassabis001.pdf Senior, A.;et al, Improved protein structure prediction using potentials from deep learning. ''Nature'' '''2020''', ''577'', 1-5]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pande002.pdf Husic, B.; et al., Markov State Models: From an Art to a Science. ''JACS'' '''2018''', ''140'', 2386-2396]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pande002.pdf Husic, B.; et al., Markov State Models: From an Art to a Science. ''JACS'' '''2018''', ''140'', 2386-2396]
  
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.mp4 Kaur, Gurlin mp4]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.mp4 Kaur, Gurlin mp4]
 
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk01.pdf  pdf]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.mp4 Sayed, Aaliya mp4]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.19.AMS535.talk02.mp4 Sayed, Aaliya mp4]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo035.pdf Allen, W. J.; et al., DOCK 6: Impact of New Features and Current Docking Performance. ''Journal of computational chemistry'' '''2015''', ''36'', 1132-1156.]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo035.pdf Allen, W. J.; et al., DOCK 6: Impact of New Features and Current Docking Performance. ''Journal of computational chemistry'' '''2015''', ''36'', 1132-1156.]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet003.pdf Mysinger, M.; et al., Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. ''Journal of medicinal chemistry'' '''2012''', ''55'', 6582-94]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet003.pdf Mysinger, M.; et al., Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. ''Journal of medicinal chemistry'' '''2012''', ''55'', 6582-94]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz002.pdf Ewing, T. J.; et al., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. ''J. Comput. Aided Mol. Des.'' '''2001''', ''15'', 411-28]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz002.pdf Ewing, T. J.; et al., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. ''J. Comput. Aided Mol. Des.'' '''2001''', ''15'', 411-28]
  
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.mp4 Urena, Jailene mp4]  
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.mp4 Urena, Jailene mp4]  
 
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk01.pdf  pdf]  
  
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.24.AMS535.talk02.mp4 Boysan, Brock mp4]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet001.pdf Irwin, J. J.; Shoichet, B. K., ZINC--a free database of commercially available compounds for virtual screening. ''J. Chem. Inf. Model.'' '''2005''', ''45'', 177-82]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet001.pdf Irwin, J. J.; Shoichet, B. K., ZINC--a free database of commercially available compounds for virtual screening. ''J. Chem. Inf. Model.'' '''2005''', ''45'', 177-82]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo022.pdf Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. ''J. Comput. Chem.'' '''2011''', ''32'', 2273-2289.]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo022.pdf Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. ''J. Comput. Chem.'' '''2011''', ''32'', 2273-2289.]
  
 
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk01.mp4 Outhwaite, Ian mp4]
 
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.26.AMS535.talk02.mp4 Marr, Douglas mp4]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet004.pdf Balius, T.E.; et al., Testing inhomogeneous solvation theory in structure-based ligand discovery. ''Proceedings of the National Academy of Sciences'' '''2017''', ''114'', 201703287.]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet004.pdf Balius, T.E.; et al., Testing inhomogeneous solvation theory in structure-based ligand discovery. ''Proceedings of the National Academy of Sciences'' '''2017''', ''114'', 201703287.]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Goodford001.pdf Goodford, P. J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. ''J. Med. Chem.'' '''1985''', ''28'', 849-57]
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kurtzman001.pdf Nguyen, C.; et al., Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. ''Journal of chemical theory and computation'' '''2014''', ''10'', 2769-2780.]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kurtzman001.pdf Nguyen, C.; et al., Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. ''Journal of chemical theory and computation'' '''2014''', ''10'', 2769-2780.]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.mp4 Li, Stan mp4]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk01.mp4 Li, Stan mp4]
 
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.10.31.AMS535.talk02.mp4 Dar, Nauroz mp4]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kubinyi002.pdf Kubinyi, H., Comparative molecular field analysis (CoMFA). ''Encyclopedia of Computational Chemistry, Databases and Expert Systems Section'', John Wiley & Sons, Ltd. '''1998''']
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kubinyi002.pdf Kubinyi, H., Comparative molecular field analysis (CoMFA). ''Encyclopedia of Computational Chemistry, Databases and Expert Systems Section'', John Wiley & Sons, Ltd. '''1998''']
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Swaan001.pdf Chang, C.; et al., Pharmacophore-based discovery of ligands for drug transporters. ''Advanced Drug Delivery Reviews'' '''2006''', ''58'', 1431-1450]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Swaan001.pdf Chang, C.; et al., Pharmacophore-based discovery of ligands for drug transporters. ''Advanced Drug Delivery Reviews'' '''2006''', ''58'', 1431-1450]
  
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bunce001.pdf Cramer, R. D.; Patterson, D. E.; Bunce, J. D., Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. ''J. Am. Chem. Soc.'', ''1988'', ''110'', 5959-5967]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bunce001.pdf Cramer, R. D.; Patterson, D. E.; Bunce, J. D., Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. ''J. Am. Chem. Soc.'', ''1988'', ''110'', 5959-5967]
 
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk01.mp4 Mannaf, Aniqa mp4]
 
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.02.AMS535.talk02.mp4 Biju, Bismi mp4]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Alvarez001.pdf Alvarez, J.; et al., Pharmacophore-Based Molecular Docking to Account for Ligand Flexibility. ''Proteins'' '''2003''', ''51'', 172-188 ]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Alvarez001.pdf Alvarez, J.; et al., Pharmacophore-Based Molecular Docking to Account for Ligand Flexibility. ''Proteins'' '''2003''', ''51'', 172-188 ]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shakhnovich001.pdf Cheron, N.; et al., OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shakhnovich001.pdf Cheron, N.; et al., OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188]
 
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk01.mp4 Kakade, Yogesh mp4]
 
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.07.AMS535.talk02.mp4 Becker, Kindra mp4]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen016.pdf Jorgensen, W.; et al., Efficient drug lead discovery and optimization. ''Acc. of Chem. Research'' '''2009''', ''42 (6)'', 724-733]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen016.pdf Jorgensen, W.; et al., Efficient drug lead discovery and optimization. ''Acc. of Chem. Research'' '''2009''', ''42 (6)'', 724-733]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pegg001.pdf Pegg, S. C.; Haresco, J. J.; Kuntz, I. D., A genetic algorithm for structure-based de novo design. ''J Comput Aided Mol Des'' '''2001''', ''15'', 911-33]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pegg001.pdf Pegg, S. C.; Haresco, J. J.; Kuntz, I. D., A genetic algorithm for structure-based de novo design. ''J Comput Aided Mol Des'' '''2001''', ''15'', 911-33]
 
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk01.mp4  Snyders, Hayden mp4]
 
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.mp4  Cheung, Andrew mp4]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.09.AMS535.talk02.mp4  Cheung, Andrew mp4]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman009.pdf Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A., Calculation of the relative change in binding free energy of a protein-inhibitor complex. ''Science'' '''1987''', ''235'', 574-6]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman009.pdf Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A., Calculation of the relative change in binding free energy of a protein-inhibitor complex. ''Science'' '''1987''', ''235'', 574-6]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/labahn001.pdf Labahn, A.; et al., Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I. ''Bioorg Med Chem.'' '''2012''', ''20'', 3446-53]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/labahn001.pdf Labahn, A.; et al., Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I. ''Bioorg Med Chem.'' '''2012''', ''20'', 3446-53]
  
 
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1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen006.pdf Jorgensen, W. L., Free Energy Calculations:  A Breakthrough for Modeling Organic Chemistry in Solution. ''Accounts Chem. Res.'' '''1989''', ''22'', 184-189]
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1&2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen006.pdf Jorgensen, W. L., Free Energy Calculations:  A Breakthrough for Modeling Organic Chemistry in Solution. ''Accounts Chem. Res.'' '''1989''', ''22'', 184-189]
  
1&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman007.pdf Kollman, P., Free Energy Calculations:  Applications to Chemical and Biochemical Phenomena. ''Chem. Rev.'' '''1993''', ''93'', 2395-2417]
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1&2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman007.pdf Kollman, P., Free Energy Calculations:  Applications to Chemical and Biochemical Phenomena. ''Chem. Rev.'' '''1993''', ''93'', 2395-2417]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lawrenz001.pdf Lawrenz, M.; et al., Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. ''J. Chem. Theory Comput.'' '''2009''', ''5'', 1106-1116]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lawrenz001.pdf Lawrenz, M.; et al., Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. ''J. Chem. Theory Comput.'' '''2009''', ''5'', 1106-1116]
 
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk01.mp4  Cordero, Ricardo mp4]
 
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.mp4  Chong, Jiyun mp4]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.14.AMS535.talk02.mp4  Chong, Jiyun mp4]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman012.pdf Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. ''Accounts Chem. Res.'' '''2000''', ''33'', 889-897]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman012.pdf Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. ''Accounts Chem. Res.'' '''2000''', ''33'', 889-897]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo019.pdf Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. ''Biochemistry'', '''2009''', ''48'', 8435-8448]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo019.pdf Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. ''Biochemistry'', '''2009''', ''48'', 8435-8448]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/bartlett000.pdf Bartlett, P. A.;  Marlowe, C. K., Evaluation of Intrinsic Binding Energy from a Hydrogen Bonding Group in an Enzyme Inhibitor. ''Science.'' '''1987''', ''235'',  569-571]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/bartlett000.pdf Bartlett, P. A.;  Marlowe, C. K., Evaluation of Intrinsic Binding Energy from a Hydrogen Bonding Group in an Enzyme Inhibitor. ''Science.'' '''1987''', ''235'',  569-571]
  
  
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.mp4 Ventura, Carlos mp4]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk01.mp4 Ventura, Carlos mp4]
 
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.mp4 Dharmajeewa, Oshini mp4]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.16.AMS535.talk02.mp4 Dharmajeewa, Oshini mp4]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo024.pdf Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, ''Biochemistry'', '''2012''', ''51'', 2390-2406]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo024.pdf Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, ''Biochemistry'', '''2012''', ''51'', 2390-2406]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Aqvist001.pdf Aqvist, J.; Mowbray, S. L., Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations. ''J Biol Chem'' '''1995''', ''270'', 9978-81]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Aqvist001.pdf Aqvist, J.; Mowbray, S. L., Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations. ''J Biol Chem'' '''1995''', ''270'', 9978-81]
  
 
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.mp4  Moy, Olivia mp4]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.21.AMS535.talk02.mp4  Moy, Olivia mp4]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen001.pdf Tominaga, Y.; Jorgensen, W. L.; General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. ''J. Med. Chem.'' '''2004''', ''47'', 2534-2549]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen001.pdf Tominaga, Y.; Jorgensen, W. L.; General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. ''J. Med. Chem.'' '''2004''', ''47'', 2534-2549]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko001.pdf Bemis, G. W.; Murcko, M. A., The properties of known drugs. 1. Molecular frameworks. ''J. Med. Chem.'' '''1996''', ''39'', 2887-93]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko001.pdf Bemis, G. W.; Murcko, M. A., The properties of known drugs. 1. Molecular frameworks. ''J. Med. Chem.'' '''1996''', ''39'', 2887-93]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko002.pdf Bemis, G. W.; Murcko, M. A., Properties of known drugs. 2. Side chains. ''J. Med. Chem.'' '''1999''', ''42'', 5095-9]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko002.pdf Bemis, G. W.; Murcko, M. A., Properties of known drugs. 2. Side chains. ''J. Med. Chem.'' '''1999''', ''42'', 5095-9]
  
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.mp4  Henderson, Max mp4]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.mp4  Henderson, Max mp4]
 
<br>
 
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk01.pdf  pdf]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.mp4  Bauer, Jack mp4]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.28.AMS535.talk02.mp4  Bauer, Jack mp4]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski002.pdf Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. ''Adv. Drug. Deliv. Rev.'' '''2001''', ''46'', 3-26]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski002.pdf Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. ''Adv. Drug. Deliv. Rev.'' '''2001''', ''46'', 3-26]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu001.pdf Hou, T. J.; Xu, X. J.; ADME evaluation in drug discovery. ''J. Mol. Model'', '''2002''', ''8'', 337-349]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu001.pdf Hou, T. J.; Xu, X. J.; ADME evaluation in drug discovery. ''J. Mol. Model'', '''2002''', ''8'', 337-349]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski001.pdf Lipinski, C. A., Chris Lipinski discusses life and chemistry after the Rule of Five. ''Drug. Discov. Today'' '''2003''', ''8'', 12-6]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski001.pdf Lipinski, C. A., Chris Lipinski discusses life and chemistry after the Rule of Five. ''Drug. Discov. Today'' '''2003''', ''8'', 12-6]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu003.pdf Hou, T. J.; Xu, X. J.; AMDE Evaluation in drug discovery 3. Modeling blood-brain barrier partitioning using simple molecular descriptors. ''J. Chem. Inf. Comput. Sci.'', '''2003''', ''43'', 2137-2152]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu003.pdf Hou, T. J.; Xu, X. J.; AMDE Evaluation in drug discovery 3. Modeling blood-brain barrier partitioning using simple molecular descriptors. ''J. Chem. Inf. Comput. Sci.'', '''2003''', ''43'', 2137-2152]
 
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.mp4  Kaur, Gurlin mp4]
 
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk01.pdf  pdf]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.mp4  Sayed, Aaliya mp4]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.11.30.AMS535.talk02.mp4  Sayed, Aaliya mp4]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Ertl2009.pdf Ertl, P.; Schuffenhauer, A.; Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. ''J. Cheminformatics'', '''2009''', ''1'', 8]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Ertl2009.pdf Ertl, P.; Schuffenhauer, A.; Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. ''J. Cheminformatics'', '''2009''', ''1'', 8]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bickerton2012.pdf Bickerton, G. R., Quantifying the chemical beauty of drugs. ''Nature Chemistry'' '''2012''', ''4'', 90-98]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bickerton2012.pdf Bickerton, G. R., Quantifying the chemical beauty of drugs. ''Nature Chemistry'' '''2012''', ''4'', 90-98]
 
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.12.05.AMS535.talk01.mp4  Urena, Jailene mp4]
 
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1. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Philpott001.pdf Hughes, J.;  et. al., Principles of early drug discovery. ''British journal of pharmacology'' '''2010''', ''162'', 1239-49.]
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1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Philpott001.pdf Hughes, J.;  et. al., Principles of early drug discovery. ''British journal of pharmacology'' '''2010''', ''162'', 1239-49.]
  
2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Weir001.pdf Waring, M.; et. al., An analysis of the attrition of drug candidates from four major pharmaceutical companies ''Nature reviews'' '''2015''', ''14''.]
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Weir001.pdf Waring, M.; et. al., An analysis of the attrition of drug candidates from four major pharmaceutical companies ''Nature reviews'' '''2015''', ''14''.]
 
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2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/ClinicalTrials.pdf Understanding Clinical Trial Terminology: What's a Phase 1, 2 OR 3 Clinical Trial?. ''www.concertpharma.com'', '''2019''']
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2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/ClinicalTrials.pdf Understanding Clinical Trial Terminology: What's a Phase 1, 2 OR 3 Clinical Trial?. ''www.concertpharma.com'', '''2019''']
[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535_thermo_cycles_study_guide.pdf Thermodynamic Cycles]  
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535_thermo_cycles_study_guide.pdf Thermodynamic Cycles]  
 
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[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535.course_topic_wrapup.pdf Course Wrap-Up Topics]
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[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535.course_topic_wrapup.pdf Course Wrap-Up Topics]
 
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Latest revision as of 17:27, 15 September 2023

Please see https://ringo.ams.stonybrook.edu/~rizzo for Rizzo Group Homepage


Instructor Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]

Brock Boysan [631-632-8519, brock dot boysan -at- stonybrook dot edu]

Course No. AMS-535 / CHE-535
Location/Time ESS 069, Monday and Wednesday 2:40PM - 4:00PM
Office Hours Anytime by appointment, Math Tower 3-129
Grading Grades will be based on the quality of:

(1) Pre-recorded oral presentations (25%)

Student will pre-record 1-2 ZOOM presentations based on papers assigned from the schedule below which will be uploaded to the class wiki for viewing by class participants

(2) Class discussion (30%)

At scheduled class times, students will attend class in person and asked to discuss the papers they have read and the presentations they have watched. For each paper, each student will prepare 2 thoughtful questions ahead of time to facilitate scientific discussion. The two questions for each paper, along with any discussion notes (if the question was discussed), will be uploaded to Google Forms by midnight of each day's class

(3) Take home quizzes (45%)

Five take home quizzes will be assigned based on the 5 major sections of the course and the lowest quiz grade will be dropped


GENERAL INFORMATION: AMS-535 provides an introduction to the field of computational structure-based drug design. The course aims to foster collaborative learning and will consist of presentations by instructors, course participants, and guest lecturers arranged in five major sections outlined below. Presentations should aim to summarize key papers, theory, and application of computational methods relevant to computational drug design. Grade will be based on oral presentations, class discussion/attendance/participation, and quizzes.


Learning Objectives

  • (1) Become informed about the field of computational structure-based drug design and the pros and cons of its methods.
  • (2) Dissect seminal theory and application papers relevant to computational drug design.
  • (3) Gain practice in giving an in-depth oral powerpoint presentation on computational drug design.
  • (4) Read, participate in discussion, and be tested across five key subject areas:
    • (i) Drug Discovery and Biomolecular Structure:
      Drug Discovery, Chemistry Review, Proteins, Carbohydrates, Nucleic acids
      Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure
    • (ii) Molecular Modeling:
      Classical Force Fields (Molecular Mechanics),
      Solvent Models, Condensed-phase Calculations, Parameter Development
    • (iii) Sampling Methods:
      Conformational Space, Molecular Dynamics (MD), Metropolis Monte Carlo (MC)
      Sampling Techniques, Predicting Protein Structure, Protein Folding
    • (iv) Lead Discovery:
      Docking as a Lead Generation Tool, Docking Algorithms
      Discovery Methods I, Discovery Methods II, Applications
    • (v) Lead Refinement:
      Free Energy Perturbation (FEP), Linear Response (LR), Extended Linear Response (ELR)
      MM-PBSA, MM-GBSA, Properties of Known Drugs, Property Prediction


LITERATURE DISCLAIMER: Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.


PRESENTATION DISCLAIMER: Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.

Syllabus Notes

This is a mixed course meaning that there will be both synchronous and asynchronous aspects. Note that course grading criteria has been modified from previous years (see grading breakdown above). Other details for this semester are as follows:

General Information:

  • We will hold class at the regularly scheduled time (M/W 2:40-4:00PM) and class will be held in person. There is no online section.
  • The first 5 lectures are to help put everyone on an even footing with regards to background material and will be given by the Instructors at the regularly scheduled class time.
  • All class correspondence should be addressed to ALL course Instructors.

Discussion Sessions:

  • The bulk of the classes will be devoted to Discussion of papers read prior to coming to class (2 per class) for which everyone will also have watched oral presentations prior to coming to class (2 per class). Oral presentations will be in the form of pre-recorded videos made by students taking the class.
  • During the Discussion sessions which are held in person the Instructors(s) will ask participants to explain details of the papers they have read which will form the basis of the "Discussion/Participation" part of their grade. Thus, it is important that everyone attend all of the classes. All students are expected to participate especially those whose papers are being discussed that day. As noted above each student will prepare two questions per paper to facilitate discussion. Your questions, and any answers that may have been discussed in class, will be uploaded into Google Forms (details to be given in class) by midnight of the day the papers are covered.
  • If a student is unable to attend a specific class for reasons beyond their control they will instead be asked to email the instructor(s) AND submit a one page Paper Summary Sheet answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Discussion" part of their grade for any synchronous classes that were missed.
  • If a students misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted.
  • Please note that this is an in-person class and all participants are expected to attend each and every class.

Oral Presentations:

  • Students will pre-record 1-2 ZOOM presentations based on papers assigned to them from the schedule shown below.
  • Students will email their pre-recorded presentations to ALL course Instructors by Friday at 5PM before the week in which their presentations will be discussed.
  • Course participants will watch the student presentations before the class in which they are to be discussed.
  • Course participants will score each student presentation using a Presentation Assessment Sheet which will be emailed to ALL Instructors within 24 hours after the class in which the presentation were discussed.

Take home Quizzes:

  • At the end of each of the five different sections of the course a take home quiz will be assigned. The "Quiz" portion of the grade will based on the four highest quiz scores attained.
  • Although the Quiz format is open book, students are expected to work alone and do their own work. Representing another person's work as your own is always wrong. The Instructors are required to report any suspected instances of academic dishonesty to the Academic Judiciary.
  • Students will have 24 hours to complete each Quiz. Late Quizzes will not be accepted.
  • Quiz question answers should integrate topics, concepts, and outcomes of the different papers covered for the section being tested.

Recording Your Oral Presentations Using Zoom: It is very straightforward to create a video of yourself giving a PPT presentation using Zoom:

  • Download the Zoom app ( https://it.stonybrook.edu/services/zoom )
  • Open the Zoom app
  • Create a new Zoom meeting with only yourself (make sure audio and video are turned on)
  • Share your screen
  • Open your paper presentation in PPT and put in presentation mode
  • Start recording and give a short test presentation to make sure that everything is working smoothly (use mouse as necessary to highlight specific regions of your slides)
  • Stop recording and quit the meeting
  • Open the newly created video (using QuickTime or some other video player) to make sure that your test presentation has both audio and video and looks good
  • Follow the above steps to create your "full-length" video presentation (videos should not exceed 20-25 minutes)
  • Email your video to ALL Instructors who will make it available to the class (please name your Zoom video Lastname_Paper1.mp4 or Lastname_Paper2.mp4 )

Oral Presentation Guidelines: Pre-recorded talks should be formal (as if at a scientific meeting or job talk), presented in PPT format, and be 20-25 minutes long. All talks will be posted on the course website. References should occur at the bottom of each slide when necessary. Presentations should be based mostly on the primary references however secondary references and other sources may be required to make some presentations complete. It is the responsibility of each presenter to email their talk by Friday at 5PM before the week in which their talk is being discussed. Talks will likely be arranged in the following order:

  • Introduction/Background (include biological relevance if applicable)
  • Specifics of the System or General Problem
  • Computational Methods (theory) and Details (system setup) being used
  • Results and Discussion (critical interpretation of results and any problems/challenges)
  • Conclusions/Future
  • Acknowledgments



-


Date
Topic
Speaker and Presentation
Primary Reference
Secondary Reference
2022.08.22 Mon
  • Organizational Meeting
Rizzo, R. mp4 Course introduction and format. Go over Syllabus. Course participant background and introductions.
-
2022.08.24 Wed

SECTION I: DRUG DISCOVERY AND BIOMOLECULAR STRUCTURE

  • Drug Discovery
1. Introduction, history, irrational vs. rational
2. Viral Target Examples

Rizzo, R. mp4

Rizzo, R. pdf

1. Jorgensen, W.L., The many roles of computation in drug discovery. Science 2004, 303, 1813-8

2. Kuntz, I. D., Structure-based strategies for drug design and discovery. Science 1992, 257, 1078-1082

-
2022.08.29 Mon
  • Chemistry Review
1. Molecular structure, bonding, graphical representations
2. Functionality, properties of organic molecules

Rizzo, R. mp4

Rizzo, R. pdf

in class lecture
-
2022.08.31 Wed
  • Biomolecular Structure
1. Lipids, carbohydrates
2. Nucleic acids, proteins

Rizzo, R. mp4

Rizzo, R. pdf

in class lecture
structures of the 20 amino acid side chains
2022.09.05 Mon
  • No Class: Labor Day
-
-
-
2022.09.07 Wed
  • Molecular Interactions and Recognition
1. Electrostatics, VDW interactions, hydrophobic effect, molecular recognition (binding energy)
2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive

Rizzo, R. mp4

Rizzo, R. pdf

in class lecture
-
2022.09.12 Mon
  • Intro. to Methods in 3-D Structure Determination
1. Crystallography, NMR
2. Structure Quality, PDB in detail

Rizzo, R. mp4

Rizzo, R. pdf

in class lecture
-
-
-
-
Take home QUIZ for Section 1 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)
-
2022.09.14 Wed

SECTION II: MOLECULAR MODELING

  • Classical Force Fields
1. All-atom Molecular Mechanics
2. OPLS

1. Outhwaite, Ian mp4
pdf

2. Marr, Douglas mp4
pdf

1. Mackerell, A. D., Jr., Empirical force fields for biological macromolecules: overview and issues. J. Comput. Chem. 2004, 25, 1584-604

2. Jorgensen, W. L.; et al., Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. J. Am. Chem. Soc. 1996, 118, 11225-11236

1. van Gunsteren, W. F.; et al., Biomolecular modeling: Goals, problems, perspectives. Angew. Chem. Int. Ed. Engl. 2006, 45, 4064-92

2. Jorgensen, W. L.; et al., The Opls Potential Functions For Proteins - Energy Minimizations For Crystals of Cyclic-Peptides and Crambin. J. Am. Chem. Soc. 1988, 110, 1657-1671

2022.09.19 Mon
  • Classical Force Fields
1. AMBER
  • Explicit Solvent Models
2. Water models (TIP3P, TIP4P, SPC)

1. Li, Stan mp4
pdf

2. Dar, Nauroz mp4
pdf

1. Cornell, W. D.; et al., A Second Generation Force Field For the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197

2. Jorgensen, W. L.; et al., Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 1983, 79, 926-935

1. Bayly, C. I.; et al., A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints For Deriving Atomic Charges - the RESP Model. J. Phys. Chem. 1993, 97, 10269-10280

2022.09.21 Wed
  • Explicit Solvent Models
1. Condensed-phase calculations (DGhydration)
  • Continuum Solvent Models
2. Generalized Born Surface Area (GBSA)

1. Mannaf, Aniqa mp4
pdf

2. Biju, Bismi mp4
pdf

1. Jorgensen, W. L.; et al., Monte Carlo Simulation of Differences in Free Energies of Hydration. J. Chem. Phys. 1985, 83, 3050-3054

2. Still, W. C.; et al., Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. J. Am. Chem. Soc 1990, 112, 6127-6129

1. Thermodynamic Cycle as Drawn By Dr. Rizzo

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2022.09.26 Mon
  • Continuum Solvent Models
1. Poisson-Boltzmann Surface Area (PBSA)
2. Accuracy of partial atomic changes for GBSA and PBSA

1. Kakade, Yogesh mp4
pdf

2. Becker, Kindra mp4
pdf

1. Sitkoff, D.; et al., Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. J. Phys. Chem. 1994, 98, 1978-1988

2. Rizzo, R. C.; et al., Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. J. Chem. Theory. Comput. 2006, 2, 128-139

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Take home QUIZ for Section 2 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)
Additional resources:

1. Duarte Ramos Matos, G.; et al., Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database. J. Chem. Eng. Data 2017, 62, 1559-1569
2. Loeffler, H. H.; et al., Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages J. Chem. Theory Comput. 2018, 14, 5567−5582

2022.09.28 Wed

SECTION III: SAMPLING METHODS

  • Molecular Conformations
1. Small molecules, peptides, relative energy, minimization methods
  • Sampling Methods for Large Simulations
2. Molecular dynamics (MD)

1. Snyders, Hayden mp4
pdf

2. Cheung, Andrew mp4
pdf

1. Howard, A. E.; Kollman, P. A., An analysis of current methodologies for conformational searching of complex molecules. J. Med. Chem. 1988, 31, 1669-75

2. Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. Nature 1990, 347, 631-9

1. Section 4 (PAGES 22-27) Colby College Molecular Mechanics Tutorial Introduction, 2004, Shattuck, T.W., Colby College

1. Holloway, M. K., A priori prediction of ligand affinity by energy minimization. Perspect. Drug Discov. Design 1998, 9-11, 63-84

2022.10.03 Mon
  • Sampling Methods for Large Simulations
1. Monte Carlo (MC)
  • Predicting Protein Structure
2. Ab initio structure prediction (protein-folding)

1. Cordero, Ricardo mp4
pdf

2. Chong, Jiyun mp4
pdf

1. Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B.

1. Jorgensen, W. L.; TiradoRives, J., Monte Carlo vs Molecular Dynamics for Conformational Sampling. J. Phys. Chem. 1996, 100,14508-14513

2. Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. Nat. Struct. Biol. 1997, 4, 10-19

1. Metropolis, N.;et al., Equation of State Calculations by Fast Computing Machines. The Journal of Chemical Physics 1953, 21, 1087-1092

2022.10.05 Wed
  • Predicting Protein Structure
1. Example Trp-cage
2. Comparative (homology) modeling

1. Ventura, Carlos mp4
pdf

2. Dharmajeewa, Oshini mp4
pdf

1. Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. J. Am. Chem. Soc. 2002, 124,11258-9

2. Marti-Renom, M. A.; et al., Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 2000,29,291-325

1. Daggett, V.; Fersht, A., The present view of the mechanism of protein folding. Nat. Rev. Mol. Cell Biol. 2003, 4, 497-502

2. Fiser, A.; et al., Evolution and physics in comparative protein structure modeling. Acc. Chem. Res. 2002, 35, 413-21

2022.10.10 Mon
  • No Class: Fall Break
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2022.10.12 Wed
  • Predicting Protein Structure
1. Case studies (CASP)
2. Accelerated MD for Blind Protein Prediction

1. No online presentation for paper #1

2. Moy, Olivia mp4
pdf

1. Moult, J., A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr. Opin. Struct. Biol. 2005,15, 285-9

2. Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. Sci. Adv. 2016, 2

1. Kryshtafovych, A.; et al., Progress over the first decade of CASP experiments. Proteins 2005, 61 Suppl 7, 225-36

2022.10.17 Mon
  • Predicting Protein Structure
1. Meso-Scale MD (Markov State Models)
2. Neural Networks

1. Henderson, Max mp4
pdf


2. Bauer, Jack mp4
pdf

1. Durrant, J.;et al, Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ACS Central Science 2020, 6, 189-196

2. Senior, A.;et al, Improved protein structure prediction using potentials from deep learning. Nature 2020, 577, 1-5

1. Husic, B.; et al., Markov State Models: From an Art to a Science. JACS 2018, 140, 2386-2396

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Take home QUIZ for Section 3 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)
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2022.10.19 Wed

SECTION IV: LEAD DISCOVERY

  • Docking
1. Introduction to DOCK
2. Test Sets (database enrichment)

1. Kaur, Gurlin mp4
pdf

2. Sayed, Aaliya mp4
pdf

1. Allen, W. J.; et al., DOCK 6: Impact of New Features and Current Docking Performance. Journal of computational chemistry 2015, 36, 1132-1156.

2. Mysinger, M.; et al., Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. Journal of medicinal chemistry 2012, 55, 6582-94

1. Ewing, T. J.; et al., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J. Comput. Aided Mol. Des. 2001, 15, 411-28

2022.10.24 Mon
  • Docking
1. Test Sets (virtual screening)
2. Footprint-based scoring

1. Urena, Jailene mp4
pdf

2. Boysan, Brock mp4
pdf


1. Irwin, J. J.; Shoichet, B. K., ZINC--a free database of commercially available compounds for virtual screening. J. Chem. Inf. Model. 2005, 45, 177-82

2. Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. J. Comput. Chem. 2011, 32, 2273-2289.

1. ZINC Website at UCSF, Shoichet group

2022.10.26 Wed
  • Docking
1. GIST score
  • Discovery Methods
2. Hotspot probes (GRID)

1. Outhwaite, Ian mp4
pdf

2. Marr, Douglas mp4
pdf

1. Balius, T.E.; et al., Testing inhomogeneous solvation theory in structure-based ligand discovery. Proceedings of the National Academy of Sciences 2017, 114, 201703287.

2. Goodford, P. J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 1985, 28, 849-57

1. Nguyen, C.; et al., Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. Journal of chemical theory and computation 2014, 10, 2769-2780.

2022.10.31 Mon
  • Discovery Methods
1. COMFA
2 Pharmacophores

1. Li, Stan mp4
pdf

2. Dar, Nauroz mp4
pdf

1. Kubinyi, H., Comparative molecular field analysis (CoMFA). Encyclopedia of Computational Chemistry, Databases and Expert Systems Section, John Wiley & Sons, Ltd. 1998

2. Chang, C.; et al., Pharmacophore-based discovery of ligands for drug transporters. Advanced Drug Delivery Reviews 2006, 58, 1431-1450

1. Cramer, R. D.; Patterson, D. E.; Bunce, J. D., Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc., 1988, 110, 5959-5967

2022.11.02 Wed
  • Discovery Methods.
1. Pharmacophores
2. De novo design

1. Mannaf, Aniqa mp4
pdf

2. Biju, Bismi mp4
pdf

1. Alvarez, J.; et al., Pharmacophore-Based Molecular Docking to Account for Ligand Flexibility. Proteins 2003, 51, 172-188

2. Cheron, N.; et al., OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. J. Med. Chem. 2016, 59, 4171-4188

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2022.11.07 Mon
  • Discovery Methods
1. De novo design
2. Genetic Algorithm

1. Kakade, Yogesh mp4
pdf

2. Becker, Kindra mp4
pdf

1. Jorgensen, W.; et al., Efficient drug lead discovery and optimization. Acc. of Chem. Research 2009, 42 (6), 724-733

2. Pegg, S. C.; Haresco, J. J.; Kuntz, I. D., A genetic algorithm for structure-based de novo design. J Comput Aided Mol Des 2001, 15, 911-33

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Take home QUIZ for Section 4 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)
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2022.11.09 Wed

SECTION V: LEAD REFINEMENT

  • Free Energy Methods
1. Thermolysin with two ligands (FEP)
2. Fatty acid synthase I ligands (TI)

1. Snyders, Hayden mp4
pdf

2. Cheung, Andrew mp4
pdf

1. Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A., Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science 1987, 235, 574-6

2. Labahn, A.; et al., Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I. Bioorg Med Chem. 2012, 20, 3446-53

1&2. Jorgensen, W. L., Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution. Accounts Chem. Res. 1989, 22, 184-189

1&2. Kollman, P., Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. Chem. Rev. 1993, 93, 2395-2417

2. Lawrenz, M.; et al., Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. J. Chem. Theory Comput. 2009, 5, 1106-1116

2022.11.14 Mon
  • MM-PB/GBSA
1. Intro to Molecular Mechanics Poisson-Boltzmann / Generalized Born Surface Area Methods
  • MM-GBSA case studies
2. EGFR and mutants

1. Cordero, Ricardo mp4
pdf

2. Chong, Jiyun mp4
pdf


1. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts Chem. Res. 2000, 33, 889-897

2. Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. Biochemistry, 2009, 48, 8435-8448

1. Bartlett, P. A.; Marlowe, C. K., Evaluation of Intrinsic Binding Energy from a Hydrogen Bonding Group in an Enzyme Inhibitor. Science. 1987, 235, 569-571


2022.11.16 Wed
  • MM-GBSA case studies
1. ErbB family selectivity
  • Linear Response
2. Intro to Linear Response (LR method)

1. Ventura, Carlos mp4
pdf

2. Dharmajeewa, Oshini mp4
pdf


1. Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, Biochemistry, 2012, 51, 2390-2406

2. Aqvist, J.; Mowbray, S. L., Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations. J Biol Chem 1995, 270, 9978-81

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2022.11.21 Mon
  • Linear Response
1. Inhibition of protein kinases (Extended LR method)
  • Properties of Known Drugs
2. Molecular Scaffolds (frameworks) and functionality (side-chains

1. No online presentation for paper #1

2. Moy, Olivia mp4
pdf


1. Tominaga, Y.; Jorgensen, W. L.; General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. J. Med. Chem. 2004, 47, 2534-2549

2. Bemis, G. W.; Murcko, M. A., The properties of known drugs. 1. Molecular frameworks. J. Med. Chem. 1996, 39, 2887-93

2. Bemis, G. W.; Murcko, M. A., Properties of known drugs. 2. Side chains. J. Med. Chem. 1999, 42, 5095-9

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2021.11.23 Wed
  • No Class: Thanksgiving
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2022.11.28 Mon
  • Properties of Known Drugs
1. Lipinski Rule of Five
2 ADME Prediction

1. Henderson, Max mp4
pdf

2. Bauer, Jack mp4
pdf

1. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug. Deliv. Rev. 2001, 46, 3-26

2. Hou, T. J.; Xu, X. J.; ADME evaluation in drug discovery. J. Mol. Model, 2002, 8, 337-349

1. Lipinski, C. A., Chris Lipinski discusses life and chemistry after the Rule of Five. Drug. Discov. Today 2003, 8, 12-6

2. Hou, T. J.; Xu, X. J.; AMDE Evaluation in drug discovery 3. Modeling blood-brain barrier partitioning using simple molecular descriptors. J. Chem. Inf. Comput. Sci., 2003, 43, 2137-2152

2022.11.30 Wed
  • Properties of Known Drugs
1. Synthetic Accessibility
2. QED

1. Kaur, Gurlin mp4
pdf

2. Sayed, Aaliya mp4
pdf

1. Ertl, P.; Schuffenhauer, A.; Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. J. Cheminformatics, 2009, 1, 8

2. Bickerton, G. R., Quantifying the chemical beauty of drugs. Nature Chemistry 2012, 4, 90-98

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2022.12.05 Mon
  • From Target to Market
1. Drug Discovery Overview
2. Attrition Rates

1. Urena, Jailene mp4
pdf

2. No online presentation for paper #2

1. Hughes, J.; et. al., Principles of early drug discovery. British journal of pharmacology 2010, 162, 1239-49.

2. Waring, M.; et. al., An analysis of the attrition of drug candidates from four major pharmaceutical companies Nature reviews 2015, 14.

2. Understanding Clinical Trial Terminology: What's a Phase 1, 2 OR 3 Clinical Trial?. www.concertpharma.com, 2019 Thermodynamic Cycles
Course Wrap-Up Topics

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Take home QUIZ for Section 5 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)
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  • Final Exam
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No Final Exam in AMS-535/CHE-535 for Fall 2022
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Required Syllabi Statements:

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