Difference between revisions of "2024 AMS-535 Fall"
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| Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com] | | Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com] | ||
− | + | Brock Boysan [631-632-8519, brock dot boysan -at- stonybrook dot edu] | |
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|- | |- | ||
| '''Course No.''' || AMS-535 / CHE-535 | | '''Course No.''' || AMS-535 / CHE-535 | ||
|- | |- | ||
− | | '''Location/Time''' || | + | | '''Location/Time''' || FREY HALL 326 WESTCAMPUS, MoWe 2:00PM - 3:20PM |
|- | |- | ||
| '''Office Hours''' || Anytime by appointment, Math Tower 3-129 | | '''Office Hours''' || Anytime by appointment, Math Tower 3-129 | ||
Line 20: | Line 19: | ||
| '''Grading''' || Grades will be based on the quality of: <br> | | '''Grading''' || Grades will be based on the quality of: <br> | ||
− | (1) | + | (1) Oral presentations (25%) |
− | ::Student will | + | ::Student will give 1-2 oral presentations (in-person) based on papers assigned from the schedule below. <br> |
− | (2) Class discussion ( | + | (2) Class discussion (25%) |
− | :: | + | ::Before each class, course participants will read the papers that are to be orally presented and come prepared to ask thoughtful questions and participate in scientific discussion about the topics being presented.<br> |
− | (3) | + | (3) Quizzes (50%) |
− | ::Five in class quizzes will be assigned based on the 5 major sections of the course and the lowest quiz grade will be dropped. | + | ::Five in class quizzes will be assigned based on the 5 major sections of the course and the lowest quiz grade will be dropped.<br> |
|- | |- | ||
|} | |} | ||
<br> | <br> | ||
+ | |||
'''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. | '''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. | ||
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== '''Syllabus Notes''' == | == '''Syllabus Notes''' == | ||
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'''General Information:''' | '''General Information:''' | ||
− | * | + | *This is an in-person course. There is no online section. |
+ | *Note that course grading criteria has been modified from previous years (see grading breakdown above). | ||
*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. | *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. | *All class correspondence should be addressed to ALL course Instructors. | ||
− | ''' | + | '''Oral Presentations:''' |
− | * | + | *Each participant will give 1-2 oral presentations (depending on the class size). |
− | * | + | *In-person presentations should be formal (as if at a scientific meeting or job talk), presented in PPT format, and be 20-25 minutes long. |
− | * | + | *All presentations will be posted on the course website. |
− | * | + | *References should occur at the bottom of each slide when necessary. |
− | *A | + | *Presentations should be based mostly on the primary references however secondary references and other sources may be required to make some presentations complete. |
− | *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 | + | *It is the responsibility of each presenter to email a PPT file of their talk by Friday at 5PM before the week in which their talk is being discussed. |
+ | *In general, talks will likely be arranged in the following order: (1) Introduction/Background (include biological relevance if applicable), (2) Specifics of the System or General Problem, (3) Computational Methods (theory) and Details (system setup) being used, (4) Results and Discussion (critical interpretation of results and any problems/challenges), (5) Conclusions/Future, and (6) Acknowledgments. | ||
+ | *Everyone in the class will evaluate each of the oral presentations using a [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.presentation.assessment.docx Presentation Assessment Sheet] | ||
+ | |||
+ | '''Class Discussion:''' | ||
+ | *A sizable portion of the course grade is based on participating in Class Discussion. Thus, it is important that everyone attend all of the classes <b> and participate in scientific discussion </b> to receive full credit. | ||
+ | *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 "Class Discussion" part of their grade for any classes that were missed. | ||
*If a student misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted. | *If a student misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted. | ||
− | ''' | + | '''Quizzes:''' |
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*Five quizzes will be used to assess student understanding of the course material. | *Five quizzes will be used to assess student understanding of the course material. | ||
− | *The quiz format is in-class, closed book. | + | *The quiz format is in-class, closed book, estimate at 30 minutes per quiz. |
*Answers to quiz questions should integrate topics, concepts, and outcomes of the different papers covered for the section being tested. | *Answers to quiz questions should integrate topics, concepts, and outcomes of the different papers covered for the section being tested. | ||
− | *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 | + | *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 and all suspected instances of academic dishonesty to the students Graduate Program Director. |
− | + | *If a student misses a quiz because of illness they must provide written documentation (Doctors Note) in order to take a makeup quiz. | |
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<br> | <br> | ||
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{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%" | {| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%" | ||
|- style="background:cornflowerblue" | |- style="background:cornflowerblue" | ||
− | | <center>'''Date'''</center> | + | | style="width: 5%" | <center>'''Date'''</center> |
− | | <center>'''Topic'''</center> | + | | style="width: 20%" | <center>'''Topic'''</center> |
− | | <center>'''Speaker and Presentation'''</center> | + | | style="width: 15%" | <center>'''Speaker and Presentation'''</center> |
− | | <center>'''Primary Reference'''</center> | + | | style="width:30%" | <center>'''Primary Reference'''</center> |
− | | <center>'''Secondary Reference'''</center> | + | | style="width: 30%" | <center>'''Secondary Reference'''</center> |
|- | |- | ||
− | | <center> | + | | <center>2024.08.26 Mon</center> |
|| | || | ||
+ | *''First Day Class'' | ||
*''Organizational Meeting'' | *''Organizational Meeting'' | ||
|| Rizzo, R | || Rizzo, R | ||
Line 128: | Line 108: | ||
|- | |- | ||
− | | <center> | + | | <center>2024.08.28 Wed</center> |
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*''Drug Discovery'' | *''Drug Discovery'' | ||
− | + | :1. Introduction, history, irrational vs. rational | |
− | + | :2. Viral Target Examples | |
− | |||
|| | || | ||
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | Rizzo, R. <br> |
− | + | lecture slides [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.08.28.ams535.rizzo.lect.001.pdf pdf] | |
|| | || | ||
− | 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] | + | :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. [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] | |
− | 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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− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.mp4 | + | Rizzo, R. <br> |
+ | prior recorded lecture 1 [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.mp4 mp4] | ||
|- | |- | ||
|- style="background:peachpuff" | |- style="background:peachpuff" | ||
− | || <center> | + | || <center>2024.09.02 Mon</center> |
||<center>-</center> | ||<center>-</center> | ||
||<center>-</center> | ||<center>-</center> | ||
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− | | <center> | + | | <center>2024.09.04 Wed</center> |
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*''Chemistry Review'' | *''Chemistry Review'' | ||
− | + | :1. Molecular structure, bonding, graphical representations | |
− | + | :2. Functionality, properties of organic molecules | |
− | |||
|| | || | ||
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | Rizzo, R. <br> |
− | || <center>in class lecture</center> | + | lecture slides [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.04.ams535.rizzo.lect.002.pdf pdf] |
+ | || | ||
+ | <center>in class lecture</center> | ||
|| | || | ||
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.mp4 | + | Rizzo, R. <br> |
+ | prior recorded lecture 2 [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.mp4 mp4] | ||
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− | | <center> | + | | <center>2024.09.09 Mon</center> |
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*''Biomolecular Structure'' | *''Biomolecular Structure'' | ||
:1. Lipids, carbohydrates | :1. Lipids, carbohydrates | ||
:2. Nucleic acids, proteins | :2. Nucleic acids, proteins | ||
− | |||
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− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | Rizzo, R. <br> |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003. | + | lecture slides [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.09.ams535.rizzo.lect.003.pdf pdf] |
− | + | || | |
− | + | <center>in class lecture</center> | |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/2010.amino_acids_scanned.pdf | + | || |
+ | Rizzo, R. <br> | ||
+ | prior recorded lecture 3 [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.mp4 mp4] | ||
+ | <br><br> | ||
+ | Structures/definitions of the 20 amino acid side chains used for this class [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/2010.amino_acids_scanned.pdf pdf] | ||
|- | |- | ||
− | + | | <center>2024.09.11 Wed</center> | |
− | | <center> | ||
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*''Molecular Interactions and Recognition'' | *''Molecular Interactions and Recognition'' | ||
Line 188: | Line 170: | ||
:2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive | :2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive | ||
|| | || | ||
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | Rizzo, R. <br> |
− | < | + | lecture slides [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.11.ams535.rizzo.lect.004.pdf pdf] |
− | <br> | + | || |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004. | + | <center>in class lecture</center> |
− | + | || | |
− | + | Rizzo, R. <br> | |
+ | prior recorded lecture 4 [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.mp4 mp4] | ||
|- | |- | ||
− | | <center> | + | | <center>2024.09.16 Mon</center> |
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*''Intro. to Methods in 3-D Structure Determination'' | *''Intro. to Methods in 3-D Structure Determination'' | ||
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:2. Structure Quality, PDB in detail | :2. Structure Quality, PDB in detail | ||
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− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | Rizzo, R. <br> |
− | < | + | lecture slides [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.16.ams535.rizzo.lect.005.pdf pdf] |
− | <br> | + | || |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | <center>in class lecture</center> |
− | + | || | |
− | + | Rizzo, R. <br> | |
+ | prior recorded lecture 5 [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.13.ams535.rizzo.lect.005.mp4 mp4] | ||
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|- style="background:lightgreen" | |- style="background:lightgreen" | ||
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||<center>-</center> | ||<center>-</center> | ||
||<center>-</center> | ||<center>-</center> | ||
− | ||<center>'''START SECTION II: MOLECULAR MODELING'''</center> | + | ||<center>-</center> |
+ | ||<center>'''START SECTION II: MOLECULAR MODELING<br> after<br>QUIZ #1'''</center> | ||
||<center>-</center> | ||<center>-</center> | ||
|- | |- | ||
− | + | | <center>2024.09.18 Wed </center> | |
− | | <center> | ||
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* ''Classical Force Fields'' | * ''Classical Force Fields'' | ||
− | :1 | + | :1. All-atom Molecular Mechanics |
− | + | || | |
− | || | + | '''QUIZ #1''' <br> <br> |
− | + | 1. Gauer, Aiden <br> | |
− | <br> | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.18.AMS535.talk01.pdf pdf] |
− | + | <br> <br> | |
− | <br> | + | || |
− | <br> | + | :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] |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/ | ||
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− | 1 | + | :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] |
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− | + | | <center>2024.09.23 Mon</center> | |
− | | <center> | + | || |
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* ''Classical Force Fields'' | * ''Classical Force Fields'' | ||
:1. OPLS | :1. OPLS | ||
:2. AMBER | :2. AMBER | ||
|| | || | ||
− | 1. | + | 1. Saha, Satyaki <br> |
− | <br> | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.23.AMS535.talk01.pdf pdf] |
− | 2. | + | <br> <br> |
− | + | 2. Fatema, Kaniz <br> | |
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.23.AMS535.talk02.pdf pdf] | ||
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− | 1. [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] | + | :1. [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] |
− | + | :2. [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. [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] | ||
− | |||
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− | 1. [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] | + | :1. [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] |
− | + | :2. [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] | |
− | 2. [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] | ||
|- | |- | ||
− | + | | <center>2024.09.25 Wed </center> | |
− | + | || | |
− | | <center> | ||
− | | | ||
*''Explicit Solvent Models'' | *''Explicit Solvent Models'' | ||
:1. Water models (TIP3P, TIP4P, SPC) | :1. Water models (TIP3P, TIP4P, SPC) | ||
:2. Condensed-phase calculations (DGhydration) | :2. Condensed-phase calculations (DGhydration) | ||
− | | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | || |
+ | 1. James, Breanna <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.25.AMS535.talk01.pdf pdf] | ||
+ | <br> <br> | ||
+ | 2. Akinboade, Modinat <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.25.AMS535.talk02.pdf pdf] | ||
+ | || | ||
+ | :1. [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] | ||
+ | :2. [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. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/DDGhyd_cycle.pdf Thermodynamic Cycle as Drawn By Dr. Rizzo] | ||
+ | |- | ||
− | + | | <center>2024.09.30 Mon</center> | |
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− | | <center> | ||
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*''Continuum Solvent Models'' | *''Continuum Solvent Models'' | ||
:1. Generalized Born Surface Area (GBSA) | :1. Generalized Born Surface Area (GBSA) | ||
:2. Poisson-Boltzmann Surface Area (PBSA) | :2. Poisson-Boltzmann Surface Area (PBSA) | ||
− | | 1. | + | || |
− | + | 1. Gebauer, Emma <br> | |
− | 2. | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.30.AMS535.talk01.pdf pdf] |
− | | 1. [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] | + | <br> <br> |
− | + | 2. <br> | |
− | 2. [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] | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.30.AMS535.talk02.pdf pdf] |
− | | | + | || |
− | | | + | :1. [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] |
+ | :2. [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] | ||
+ | || | ||
<center>-</center> | <center>-</center> | ||
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− | ||<center>''' | + | ||<center>''''START SECTION III: SAMPLING METHODS <br> after <br> QUIZ #2'''</center> |
− | ||<center> | + | ||<center>-</center> |
− | |||
− | |||
|- | |- | ||
− | | <center> | + | | <center>2024.10.02 Wed </center> |
|| | || | ||
− | |||
*''Molecular Conformations'' | *''Molecular Conformations'' | ||
:1. Small molecules, peptides, relative energy, minimization methods | :1. Small molecules, peptides, relative energy, minimization methods | ||
− | + | || | |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/ | + | '''QUIZ #2''' <br> <br> |
− | + | 1. Averkava, Veranika <br> | |
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.02.AMS535.talk01.pdf pdf] | ||
+ | <br> <br> | ||
+ | || | ||
+ | :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] | ||
+ | || | ||
+ | :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. [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] | ||
+ | |- | ||
− | + | | <center>2024.10.07 Mon </center> | |
− | + | || | |
− | |||
− | |||
− | |||
− | |||
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− | |||
− | |||
− | |||
− | |||
*''Sampling Methods for Large Simulations'' | *''Sampling Methods for Large Simulations'' | ||
:1. Molecular dynamics (MD) | :1. Molecular dynamics (MD) | ||
:2. Monte Carlo (MC) | :2. Monte Carlo (MC) | ||
− | + | || | |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | 1. Lu, Hongbo <br>[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.07.AMS535.talk01.pdf pdf] |
+ | <br> <br> | ||
+ | 2. Kalinowski, Nicole <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.07.AMS535.talk02.pdf pdf] | ||
+ | || | ||
+ | :1. [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] | ||
+ | :2. [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.] | ||
+ | || | ||
+ | :2. [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. [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] | ||
+ | |- | ||
− | + | | <center>2024.10.09 Wed </center> | |
− | + | || | |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
*''Predicting Protein Structure'' | *''Predicting Protein Structure'' | ||
:1. Ab initio structure prediction (protein-folding) | :1. Ab initio structure prediction (protein-folding) | ||
− | |||
:2. Example Trp-cage | :2. Example Trp-cage | ||
− | + | || | |
+ | 1. Kennedy, Christopher <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.09.AMS535.talk01.pdf pdf] | ||
+ | <br> <br> | ||
+ | 2. Jordan, Claire <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.09.AMS535.talk02.pdf pdf] | ||
+ | || | ||
+ | :1. [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] | ||
+ | :2. [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. [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. [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] | ||
+ | |- | ||
− | + | |- style="background:peachpuff" | |
− | + | || <center>2024.10.14 Mon</center> | |
− | + | || <center>-</center> | |
− | + | || <center>-</center> | |
+ | ||<center>'''NO CLASS - FALL BREAK'''</center> | ||
+ | || <center>-</center> | ||
+ | |- | ||
− | + | | <center>2024.10.16 Wed</center> | |
− | + | || | |
− | |||
− | |||
*''Predicting Protein Structure'' | *''Predicting Protein Structure'' | ||
:1. Comparative (homology) modeling | :1. Comparative (homology) modeling | ||
− | :2. | + | :2. Accelerated MD for Blind Protein Prediction |
− | + | || | |
+ | 1. Behboodian, Ali <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.16.AMS535.talk01.pdf pdf] | ||
+ | <br> <br> | ||
+ | 2. Parwana, Diksha <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.16.AMS535.talk02.pdf pdf] | ||
+ | || | ||
+ | :1. [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] | ||
+ | :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''] | ||
+ | || <center>-</center> | ||
+ | |- | ||
− | + | | <center>2024.10.21 Mon</center> | |
− | + | || | |
− | |||
− | |||
− | |||
− | |||
− | |||
*''Predicting Protein Structure'' | *''Predicting Protein Structure'' | ||
− | :1. | + | :1. Alpha Fold |
:2. Meso-Scale MD (Markov State Models) | :2. Meso-Scale MD (Markov State Models) | ||
− | + | || | |
− | + | 1. Bickel, John <br> | |
− | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.21.AMS535.talk01.pdf pdf] | |
− | 2. | + | <br> <br> |
− | + | 2. Bickel, John <br> | |
− | 2. [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] | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.21.AMS535.talk02.pdf pdf] |
− | + | || | |
+ | :1. [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] | ||
+ | :2. [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. [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] | ||
|- | |- | ||
Line 385: | Line 379: | ||
||<center>-</center> | ||<center>-</center> | ||
||<center>-</center> | ||<center>-</center> | ||
− | ||<center>''' | + | ||<center>'''START SECTION IV: LEAD DISCOVERY <br> after <br> QUIZ #3'''</center> |
||<center>-</center> | ||<center>-</center> | ||
|- | |- | ||
− | | <center> | + | | <center>2024.10.23 Wed </center> |
|| | || | ||
'''SECTION IV: LEAD DISCOVERY''' | '''SECTION IV: LEAD DISCOVERY''' | ||
*''Docking'' | *''Docking'' | ||
:1. Introduction to DOCK | :1. Introduction to DOCK | ||
− | + | || | |
+ | '''QUIZ #3''' <br> <br> | ||
+ | 1. O'Reilly, Owen <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.23.AMS535.talk01.pdf pdf] | ||
+ | <br> <br> | ||
+ | || | ||
+ | :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.] | ||
+ | || | ||
+ | :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] | ||
+ | |- | ||
− | + | | <center>2024.10.28 Mon</center> | |
− | + | || | |
− | + | *''Docking'' | |
− | |||
− | |||
:1. Test Sets (database enrichment) | :1. Test Sets (database enrichment) | ||
:2. Test Sets (virtual screening) | :2. Test Sets (virtual screening) | ||
− | + | || | |
+ | 1. Corbo, Chris <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.28.AMS535.talk01.pdf pdf] | ||
+ | <br> <br> | ||
+ | 2.Corbo, Chris <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.28.AMS535.talk02.pdf pdf]] | ||
+ | || | ||
+ | :1. [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] | ||
+ | :2. [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. [https://zinc.docking.org ZINC Website at UCSF, Shoichet group] | ||
+ | |- | ||
− | + | | <center>2024.10.30 Wed</center> | |
− | + | || | |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
*''Docking'' | *''Docking'' | ||
:1. Footprint-based scoring | :1. Footprint-based scoring | ||
Line 418: | Line 424: | ||
*''Discovery Methods'' | *''Discovery Methods'' | ||
:2. Hotspot probes (GRID) | :2. Hotspot probes (GRID) | ||
− | + | || | |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | 1. Boysan, Brock <br> |
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.30.AMS535.talk01.pdf pdf] | ||
+ | <br> <br> | ||
+ | 2. Boysan, Brock <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.30.AMS535.talk02.pdf pdf] | ||
+ | || | ||
+ | :1. [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.] | ||
+ | :2. [https://ringo.ams.stonybrook.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] | ||
+ | ||<center>-</center> | ||
+ | |- | ||
− | + | | <center>2024.11.04 Mon</center> | |
− | + | || | |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
*''Discovery Methods'' | *''Discovery Methods'' | ||
:1. COMFA | :1. COMFA | ||
− | :2 Pharmacophores | + | :2. Pharmacophores |
− | + | || | |
+ | 1. Okisamen, Benjamin <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.04.AMS535.talk01.pdf pdf] | ||
+ | <br> <br> | ||
+ | 2. Rufrano, Michael <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.04.AMS535.talk02.pdf pdf] | ||
+ | || | ||
+ | :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. [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] | ||
+ | || | ||
+ | :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] | ||
+ | |- | ||
− | + | | <center>2024.11.06 Wed</center> | |
− | + | || | |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
*''Discovery Methods.'' | *''Discovery Methods.'' | ||
:1. Pharmacophores | :1. Pharmacophores | ||
:2. De novo design | :2. De novo design | ||
− | + | || | |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | 1. Rosenn, Eric <br> |
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.06.AMS535.talk01.pdf pdf] | ||
+ | <br> <br> | ||
+ | 2. Spector, Evan <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.06.AMS535.talk02.pdf pdf] | ||
+ | || | ||
+ | :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. [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] | ||
+ | ||<center>-</center> | ||
+ | |- | ||
− | + | | <center>2024.11.11 Mon</center> | |
− | + | || | |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
*''Discovery Methods'' | *''Discovery Methods'' | ||
:1. De novo design | :1. De novo design | ||
:2. Genetic Algorithm | :2. Genetic Algorithm | ||
− | + | || | |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | 1. Pak, Steven <br> |
− | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.11.AMS535.talk01.pdf pdf] | |
− | 2. | + | <br> <br> |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | 2. Ogunfolakan, Oyindamola <br> |
− | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.11.AMS535.talk02.pdf pdf] | |
− | + | || | |
− | + | :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. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/PrentisSingleton001.pdf Prentis, L and Singleton, C et al.; A molecular evolution algorithm for ligand design in DOCK ''J Comp Chem'' '''2022''', ''43 (29)'', 1942-1963] | |
− | 2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/PrentisSingleton001.pdf Prentis, L and Singleton, C et al.; A molecular evolution algorithm for ligand design in DOCK ''J Comp Chem'' '''2022''', ''43 (29)'', 1942-1963] | ||
− | |||
||<center>-</center> | ||<center>-</center> | ||
|- | |- | ||
Line 478: | Line 492: | ||
||<center>-</center> | ||<center>-</center> | ||
||<center>-</center> | ||<center>-</center> | ||
− | ||<center>''' | + | ||<center>'''START SECTION V: LEAD REFINEMENT <br> after <br> QUIZ #4'''</center> |
||<center>-</center> | ||<center>-</center> | ||
|- | |- | ||
− | | <center> | + | | <center>2024.11.13 Wed </center> |
|| | || | ||
− | |||
*''Free Energy Methods'' | *''Free Energy Methods'' | ||
:1. Thermolysin with two ligands (FEP) | :1. Thermolysin with two ligands (FEP) | ||
− | + | || | |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | '''QUIZ #4''' <br> <br> |
− | + | 1. Wray, Zahra <br> | |
− | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.13.AMS535.talk01.pdf pdf] | |
− | + | <br> <br> | |
− | 1. [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. [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] | |
− | 1. [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] | + | || |
+ | :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] | ||
+ | :1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/tronrud002.pdf Tronrud, D.E.; Holden, H.M.; Matthews, B.W.; Structures of Two Thermolysin-Inhibitor Complexes That Differ by a Single Hydrogen Bond. ''Science'' '''1987''', ''235'', 571-573] | ||
+ | :1. [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. [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] | ||
|- | |- | ||
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+ | | <center>2024.11.18 Mon</center> | ||
+ | || | ||
+ | *''Thermodynamic Integration'' | ||
+ | :1. Fatty acid synthase I ligands | ||
*'' MM-PB/GBSA'' | *'' MM-PB/GBSA'' | ||
:2. Intro to Molecular Mechanics Poisson-Boltzmann / Generalized Born Surface Area Methods | :2. Intro to Molecular Mechanics Poisson-Boltzmann / Generalized Born Surface Area Methods | ||
− | + | || | |
+ | 1. Seecharan, Vanie <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.18.AMS535.talk01.pdf pdf] | ||
+ | <br> <br> | ||
+ | 2. Hailegeorgis, Derara <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.18.AMS535.talk02.pdf pdf] | ||
+ | || | ||
+ | :1. [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] | ||
+ | :2. [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] | ||
+ | || | ||
+ | :1. [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] | ||
+ | |- | ||
− | + | | <center>2024.11.20 Wed </center> | |
− | + | || | |
− | + | *''MM-GBSA case studies" | |
− | + | :1. EGFR and mutants | |
− | + | :2. ErbB family selectivity | |
− | + | || | |
− | + | 1. Rizzo, Rob <br> | |
− | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.20.AMS535.talk01.pdf pdf] | |
− | 2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/ | + | <br> <br> |
− | | | + | 2. Rizzo, Rob <br> |
− | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.20.AMS535.talk02.pdf pdf] | |
− | + | || | |
− | + | :1. [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] | |
− | + | :2. [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] | |
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− | + | | <center>2024.11.25 Mon </center> | |
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*''Linear Response'' | *''Linear Response'' | ||
:1. Intro to Linear Response (LR method) | :1. Intro to Linear Response (LR method) | ||
:2. Inhibition of protein kinases (Extended LR method) | :2. Inhibition of protein kinases (Extended LR method) | ||
− | + | || | |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | 1. Kwan, Isabelle <br> |
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.25.AMS535.talk01.pdf pdf] | ||
+ | <br> <br> | ||
+ | 2. Reisel, Alexander <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.25.AMS535.talk02.pdf pdf] | ||
+ | || | ||
+ | :1. [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] | ||
+ | :2. [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] | ||
+ | || <center>-</center> | ||
+ | |- | ||
− | + | |- style="background:peachpuff" | |
− | + | | <center>2024.11.27 Wed</center> | |
− | + | || <center>-</center> | |
+ | || <center>-</center> | ||
+ | || <center> '''NO CLASS: THANKSGIVING''' </center> | ||
+ | || <center>-</center> | ||
+ | |- | ||
− | + | | <center>2024.12.02 Mon </center> | |
− | + | || | |
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*''Properties of Known Drugs'' | *''Properties of Known Drugs'' | ||
:1. Molecular Scaffolds (frameworks) and functionality (side-chains) | :1. Molecular Scaffolds (frameworks) and functionality (side-chains) | ||
:2. Lipinski Rule of Five | :2. Lipinski Rule of Five | ||
− | + | || | |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | 1. Boysan, Brock <br> |
− | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.12.02.AMS535.talk01.pdf pdf] | |
− | 2. | + | <br> <br> |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | 2. Boysan, Brock <br> |
− | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.12.02.AMS535.talk02.pdf pdf] | |
− | + | || | |
− | 1. [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] | + | :1. [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] |
− | + | :1. [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] | |
− | 2. [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. [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. [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] | ||
|- | |- | ||
− | | <center> | + | |
− | + | | <center>2024.12.04 Wed </center> | |
+ | || | ||
*''Properties of Known Drugs'' | *''Properties of Known Drugs'' | ||
+ | :1. Drug likeness | ||
+ | :2. Descriptor-driven design | ||
+ | || | ||
+ | 1. Pak, Steven <br> | ||
− | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.12.04.AMS535.talk01.pdf pdf] | |
− | + | <br> <br> | |
− | + | 2. Pak, Steven <br> | |
− | |||
− | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.12.04.AMS535.talk02.pdf pdf] | |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/ | + | || |
− | + | :1. [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] | |
+ | :2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/matos_pak_2023.pdf Matos, DRG; Pak, S; Rizzo R; Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit. ''J. Chem. Inf. Model.'' '''2023'''] | ||
+ | || | ||
+ | |- | ||
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||<center>-</center> | ||<center>-</center> | ||
− | | | + | ||<center>'''Class Wrap up <br> after <br> QUIZ #5'''</center> |
− | + | ||<center>-</center> | |
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− | <br> | ||
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|- | |- | ||
− | + | | <center>2024.12.09 Mon </center> | |
− | + | || | |
− | |<center> | + | *''Last Day Class'' |
− | || | + | ||'''QUIZ #5''' <br> <br> |
− | *''''' | ||
||<center>-</center> | ||<center>-</center> | ||
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|- | |- |
Latest revision as of 11:23, 9 October 2024
Please see https://ringo.ams.stonybrook.edu/~rizzo for Rizzo Group Homepage
Instructors | Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com]
Brock Boysan [631-632-8519, brock dot boysan -at- stonybrook dot edu] |
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Course No. | AMS-535 / CHE-535 |
Location/Time | FREY HALL 326 WESTCAMPUS, MoWe 2:00PM - 3:20PM |
Office Hours | Anytime by appointment, Math Tower 3-129 |
Grading | Grades will be based on the quality of: (1) Oral presentations (25%)
(2) Class discussion (25%)
(3) Quizzes (50%)
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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
- (i) Drug Discovery and Biomolecular Structure:
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
General Information:
- This is an in-person course. There is no online section.
- Note that course grading criteria has been modified from previous years (see grading breakdown above).
- 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.
Oral Presentations:
- Each participant will give 1-2 oral presentations (depending on the class size).
- In-person presentations should be formal (as if at a scientific meeting or job talk), presented in PPT format, and be 20-25 minutes long.
- All presentations 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 a PPT file of their talk by Friday at 5PM before the week in which their talk is being discussed.
- In general, talks will likely be arranged in the following order: (1) Introduction/Background (include biological relevance if applicable), (2) Specifics of the System or General Problem, (3) Computational Methods (theory) and Details (system setup) being used, (4) Results and Discussion (critical interpretation of results and any problems/challenges), (5) Conclusions/Future, and (6) Acknowledgments.
- Everyone in the class will evaluate each of the oral presentations using a Presentation Assessment Sheet
Class Discussion:
- A sizable portion of the course grade is based on participating in Class Discussion. Thus, it is important that everyone attend all of the classes and participate in scientific discussion to receive full credit.
- 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 "Class Discussion" part of their grade for any classes that were missed.
- If a student misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted.
Quizzes:
- Five quizzes will be used to assess student understanding of the course material.
- The quiz format is in-class, closed book, estimate at 30 minutes per quiz.
- Answers to quiz questions should integrate topics, concepts, and outcomes of the different papers covered for the section being tested.
- 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 and all suspected instances of academic dishonesty to the students Graduate Program Director.
- If a student misses a quiz because of illness they must provide written documentation (Doctors Note) in order to take a makeup quiz.
Class Schedule
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Required Syllabi Statements:
The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php
Student Accessibility Support Center Statement: If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.
Academic Integrity Statement: Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html
Critical Incident Management: Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php