Difference between revisions of "2024 AMS-535 Fall"
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*Each participant will give 1-2 oral presentations (depending on the class size). | *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. | *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 | + | *All presentations will be posted on the course website. |
*References should occur at the bottom of each slide when necessary. | *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. | *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. | *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. | + | *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:''' | '''Class Discussion:''' | ||
Line 72: | Line 73: | ||
'''Quizzes:''' | '''Quizzes:''' | ||
*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 and all suspected instances of academic dishonesty to the students Graduate Program Director. | *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. | ||
<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 105: | Line 108: | ||
|- | |- | ||
− | | <center> | + | | <center>2024.08.28 Wed</center> |
|| | || | ||
*''Drug Discovery'' | *''Drug Discovery'' | ||
Line 111: | Line 114: | ||
:2. Viral Target Examples | :2. Viral Target Examples | ||
|| | || | ||
− | Rizzo, R. lecture slides [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] | ||
|| | || | ||
− | Rizzo, R. 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] | + | 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'' | ||
Line 133: | Line 138: | ||
:2. Functionality, properties of organic molecules | :2. Functionality, properties of organic molecules | ||
|| | || | ||
− | Rizzo, R. lecture slides [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/2024.09.04.ams535.rizzo.lect.002.pdf pdf] | ||
|| | || | ||
<center>in class lecture</center> | <center>in class lecture</center> | ||
|| | || | ||
− | Rizzo, R. 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] | + | 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] | ||
|- | |- | ||
− | | <center> | + | | <center>2024.09.09 Mon</center> |
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*''Biomolecular Structure'' | *''Biomolecular Structure'' | ||
Line 146: | Line 153: | ||
:2. Nucleic acids, proteins | :2. Nucleic acids, proteins | ||
|| | || | ||
− | Rizzo, R. lecture slides [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/2024.09.09.ams535.rizzo.lect.003.pdf pdf] | ||
|| | || | ||
<center>in class lecture</center> | <center>in class lecture</center> | ||
|| | || | ||
− | Rizzo, R. 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] | + | 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> | <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] | 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> | ||
|| | || | ||
*''Molecular Interactions and Recognition'' | *''Molecular Interactions and Recognition'' | ||
Line 162: | 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 | ||
|| | || | ||
− | Rizzo, R. lecture slides [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] | ||
|| | || | ||
<center>in class lecture</center> | <center>in class lecture</center> | ||
|| | || | ||
− | Rizzo, R. 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] | + | 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'' | ||
Line 175: | Line 185: | ||
:2. Structure Quality, PDB in detail | :2. Structure Quality, PDB in detail | ||
|| | || | ||
− | Rizzo, R. lecture slides [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] | ||
|| | || | ||
<center>in class lecture</center> | <center>in class lecture</center> | ||
|| | || | ||
− | Rizzo, R. 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] | + | 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] | ||
|- | |- | ||
Line 189: | Line 201: | ||
||<center>-</center> | ||<center>-</center> | ||
|- | |- | ||
− | | <center> | + | | <center>2024.09.18 Wed </center> |
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* ''Classical Force Fields'' | * ''Classical Force Fields'' | ||
:1. All-atom Molecular Mechanics | :1. All-atom Molecular Mechanics | ||
− | |||
− | |||
|| | || | ||
− | :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] | + | '''QUIZ #1''' <br> <br> |
+ | 1. Gauer, Aiden <br> | ||
+ | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.18.AMS535.talk01.pdf pdf] | ||
+ | <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] | ||
|| | || | ||
: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] | :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] | ||
|- | |- | ||
− | + | | <center>2024.09.23 Mon</center> | |
− | | <center> | ||
|| | || | ||
* ''Classical Force Fields'' | * ''Classical Force Fields'' | ||
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:2. AMBER | :2. AMBER | ||
|| | || | ||
− | + | 1. Saha, Satyaki <br> | |
− | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.23.AMS535.talk01.pdf pdf] | |
+ | <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] | ||
|| | || | ||
: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] | ||
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|- | |- | ||
− | | <center> | + | | <center>2024.09.25 Wed </center> |
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*''Explicit Solvent Models'' | *''Explicit Solvent Models'' | ||
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:2. Condensed-phase calculations (DGhydration) | :2. Condensed-phase calculations (DGhydration) | ||
|| | || | ||
− | + | 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] | :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] | ||
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|- | |- | ||
− | | <center> | + | | <center>2024.09.30 Mon</center> |
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*''Continuum Solvent Models'' | *''Continuum Solvent Models'' | ||
Line 239: | Line 259: | ||
:2. Poisson-Boltzmann Surface Area (PBSA) | :2. Poisson-Boltzmann Surface Area (PBSA) | ||
|| | || | ||
− | + | 1. Gebauer, Emma <br> | |
− | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.30.AMS535.talk01.pdf pdf] | |
+ | <br> <br> | ||
+ | 2. <br> | ||
+ | [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] | :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] | ||
Line 256: | Line 279: | ||
|- | |- | ||
− | | <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 | ||
|| | || | ||
− | + | '''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/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] | ||
Line 267: | Line 293: | ||
: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/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] | :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> | + | | <center>2024.10.07 Mon </center> |
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*''Sampling Methods for Large Simulations'' | *''Sampling Methods for Large Simulations'' | ||
Line 282: | Line 301: | ||
:2. Monte Carlo (MC) | :2. Monte Carlo (MC) | ||
|| | || | ||
− | + | 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] | :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] | ||
Line 293: | Line 313: | ||
|- | |- | ||
− | | <center> | + | | <center>2024.10.09 Wed </center> |
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*''Predicting Protein Structure'' | *''Predicting Protein Structure'' | ||
Line 299: | Line 319: | ||
: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] | :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] | ||
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|- | |- | ||
− | | <center> | + | |- 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] | :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/ | + | :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>-</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] | |
+ | <br> <br> | ||
+ | 2. Bickel, John <br> | ||
+ | [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/ | + | :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/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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− | | <center> | + | | <center>2024.10.23 Wed </center> |
|| | || | ||
'''SECTION IV: LEAD DISCOVERY''' | '''SECTION IV: LEAD DISCOVERY''' | ||
Line 352: | Line 389: | ||
: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/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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|- | |- | ||
− | | <center> | + | | <center>2024.10.28 Mon</center> |
|| | || | ||
*''Docking'' | *''Docking'' | ||
Line 365: | Line 405: | ||
: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] | :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] | ||
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|- | |- | ||
− | | <center> | + | | <center>2024.10.30 Wed</center> |
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*''Docking'' | *''Docking'' | ||
Line 382: | Line 425: | ||
:2. Hotspot probes (GRID) | :2. Hotspot probes (GRID) | ||
|| | || | ||
− | + | 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.] | :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.] | ||
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|- | |- | ||
− | | <center> | + | | <center>2024.11.04 Mon</center> |
|| | || | ||
*''Discovery Methods'' | *''Discovery Methods'' | ||
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: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'''] | :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'''] | ||
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|- | |- | ||
− | | <center> | + | | <center>2024.11.06 Wed</center> |
|| | || | ||
*''Discovery Methods.'' | *''Discovery Methods.'' | ||
Line 411: | Line 460: | ||
:2. De novo design | :2. De novo design | ||
|| | || | ||
− | + | 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 ] | :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 ] | ||
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|- | |- | ||
− | | <center> | + | | <center>2024.11.11 Mon</center> |
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*''Discovery Methods'' | *''Discovery Methods'' | ||
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:2. Genetic Algorithm | :2. Genetic Algorithm | ||
|| | || | ||
− | + | 1. Pak, Steven <br> | |
− | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.11.AMS535.talk01.pdf pdf] | |
+ | <br> <br> | ||
+ | 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] | :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] | ||
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|- | |- | ||
− | | <center> | + | | <center>2024.11.13 Wed </center> |
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*''Free Energy Methods'' | *''Free Energy Methods'' | ||
:1. Thermolysin with two ligands (FEP) | :1. Thermolysin with two ligands (FEP) | ||
|| | || | ||
− | 1. | + | '''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/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/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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− | | <center> | + | | <center>2024.11.18 Mon</center> |
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*''Thermodynamic Integration'' | *''Thermodynamic Integration'' | ||
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: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] | :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] | ||
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|- | |- | ||
− | + | | <center>2024.11.20 Wed </center> | |
− | | <center> | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
|| | || | ||
*''MM-GBSA case studies" | *''MM-GBSA case studies" | ||
Line 486: | Line 539: | ||
:2. ErbB family selectivity | :2. ErbB family selectivity | ||
|| | || | ||
− | + | 1. Rizzo, Rob <br> | |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.20.AMS535.talk01.pdf pdf] |
− | + | <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] | :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] | ||
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|- | |- | ||
− | | <center> | + | | <center>2024.11.25 Mon </center> |
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*''Linear Response'' | *''Linear Response'' | ||
Line 501: | Line 556: | ||
:2. Inhibition of protein kinases (Extended LR method) | :2. Inhibition of protein kinases (Extended LR method) | ||
|| | || | ||
− | + | 1. Kwan, Isabelle <br> | |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.25.AMS535.talk01.pdf pdf] |
− | + | <br> <br> | |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | 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] | :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] | ||
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|- | |- | ||
− | | <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> | ||
|| | || | ||
*''Properties of Known Drugs'' | *''Properties of Known Drugs'' | ||
Line 517: | Line 581: | ||
:2. Lipinski Rule of Five | :2. Lipinski Rule of Five | ||
|| | || | ||
− | + | 1. Boysan, Brock <br> | |
− | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.12.02.AMS535.talk01.pdf pdf] | |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | <br> <br> |
+ | 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/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/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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|- | |- | ||
− | | <center> | + | | <center>2024.12.04 Wed </center> |
|| | || | ||
*''Properties of Known Drugs'' | *''Properties of Known Drugs'' | ||
− | :1. | + | :1. Drug likeness |
− | :2. | + | :2. Descriptor-driven design |
|| | || | ||
− | + | 1. Pak, Steven <br> | |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | |
− | + | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.12.04.AMS535.talk01.pdf pdf] | |
− | [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/ | + | <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] | ||
|| | || | ||
− | :1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/ | + | :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'''] | :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>2024.12.09 Mon </center> |
− | + | || | |
− | + | *''Last Day Class'' | |
+ | ||'''QUIZ #5''' <br> <br> | ||
||<center>-</center> | ||<center>-</center> | ||
||<center>-</center> | ||<center>-</center> |
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] |
---|---|
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%)
|
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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Rizzo, R | Course introduction and format. Go over Syllabus. Course participant background and introductions. | |
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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