Difference between revisions of "2021 AMS-535 Fall"

Latest revision as of 20:11, 3 December 2021

Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage

Instructor	Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com] Chris Corbo [631-632-8519, christopher dot corbo -at- stonybrook dot edu]
Course No.	AMS-535 / CHE-535
Location/Time	Online, Monday and Wednesday 2:40PM - 4:00PM
Office Hours	Anytime by appointment, Math Tower 3-129
Grading	Grades will be based on the quality of: (1) Pre-recorded oral presentations (25%) Student will pre-record 2 ZOOM presentations based on papers assigned from the schedule below (2) Class discussion (30%) At scheduled class times students will be assigned into ZOOM breakout rooms and asked to discuss the papers they have read and the presentations they have watched (3) Take home quizzes (45%) Five take home quizzes will be assigned based on the 5 major sections of the course and the lowest quiz grade will be dropped

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

Learning Objectives

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

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

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

Online Syllabus Notes

As a result of the COVID-19 outbreak this course is being offered online. This is a mixed course meaning that there will be both synchronous and asynchronous aspects. Note that course grading criteria has been modified from previous years (see grading breakdown above). Other details for this semester are as follows:

General Information:

We will hold class at the regularly scheduled time (M/W 2:40-4:00PM) however this will be done online via ZOOM.
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 and will be made available on the class website.
All class correspondence should be addressed to ALL course Instructors.

Discussion Sessions:

The bulk of the classes will be devoted to Discussion of papers read prior to coming to class (2 per class) for which everyone will also have watched oral presentations prior to coming to class (2 per class). Oral presentations will be in the form of pre-recorded videos made by students taking the class.
During the Discussion sessions (ZOOM breakout rooms) the Instructors will ask participants to explain details of the papers they have read which will form the basis of the "Discussion" part of their grade. Thus, it is important that everyone attend all of the synchronous classes. All students are expected to participate especially those whose papers are being discussed that day. Breakout room discussion will NOT be recorded.
If a student is unable to attend an online class they will instead be asked to submit a one page Paper Summary Sheet answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Discussion" part of their grade for any synchronous classes that were missed.
If a students misses an online class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted.

Oral Presentations:

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

Take home Quizzes:

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

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

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

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

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

-

Date	Topic	Speaker and Presentation	Primary Reference	Secondary Reference
2021.08.23 Mon	Organizational Meeting	Rizzo, R. mp4	Course introduction and format. Go over Syllabus. Course participant background and introductions.	-
2021.08.25 Wed	SECTION I: DRUG DISCOVERY AND BIOMOLECULAR STRUCTURE Drug Discovery 1. Introduction, history, irrational vs. rational 2. Viral Target Examples	Rizzo, R. mp4 Rizzo, R. pdf	1. Jorgensen, W.L., The many roles of computation in drug discovery. Science 2004, 303, 1813-8 2. Kuntz, I. D., Structure-based strategies for drug design and discovery. Science 1992, 257, 1078-1082	-
2021.08.30 Mon	Chemistry Review 1. Molecular structure, bonding, graphical representations 2. Functionality, properties of organic molecules	Rizzo, R. mp4 Rizzo, R. pdf	presentation	-
2021.09.01 Wed	Biomolecular Structure 1. Lipids, carbohydrates 2. Nucleic acids, proteins	Rizzo, R. mp4 Rizzo, R. pdf	presentation	structures of the 20 amino acid side chains
2021.09.06 Mon	No Class: Labor Day	-	-	-
2021.09.08 Wed	Molecular Interactions and Recognition 1. Electrostatics, VDW interactions, hydrophobic effect, molecular recognition (binding energy) 2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive	Rizzo, R. mp4 Rizzo, R. pdf	presentation	-
2021.09.13 Mon	Intro. to Methods in 3-D Structure Determination 1. Crystallography, NMR 2. Structure Quality, PDB in detail	Rizzo, R. mp4 Rizzo, R. pdf	presentation	-
-	-	-	Take home QUIZ for Section 1 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)	-
2021.09.15 Wed	SECTION II: MOLECULAR MODELING Classical Force Fields 1. All-atom Molecular Mechanics 2. OPLS	1. Feltman, Scott mp4 pdf 2. Boysan, Brock mp4 pdf	1. Mackerell, A. D., Jr., Empirical force fields for biological macromolecules: overview and issues. J. Comput. Chem. 2004, 25, 1584-604 2. Jorgensen, W. L.; et al., Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. J. Am. Chem. Soc. 1996, 118, 11225-11236	1. van Gunsteren, W. F.; et al., Biomolecular modeling: Goals, problems, perspectives. Angew. Chem. Int. Ed. Engl. 2006, 45, 4064-92 2. Jorgensen, W. L.; et al., The Opls Potential Functions For Proteins - Energy Minimizations For Crystals of Cyclic-Peptides and Crambin. J. Am. Chem. Soc. 1988, 110, 1657-1671
2021.09.20 Mon	Classical Force Fields 1. AMBER Explicit Solvent Models 2. Water models (TIP3P, TIP4P, SPC)	1. Yearsley, Matthew mp4 pdf 2. Joshi, Anuja-Ria mp4 pdf	1. Cornell, W. D.; et al., A Second Generation Force Field For the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197 2. Jorgensen, W. L.; et al., Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 1983, 79, 926-935	1. Bayly, C. I.; et al., A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints For Deriving Atomic Charges - the RESP Model. J. Phys. Chem. 1993, 97, 10269-10280
2021.09.22 Wed	Explicit Solvent Models 1. Condensed-phase calculations (DGhydration) Continuum Solvent Models 2. Generalized Born Surface Area (GBSA)	1. Delamonica, Brenda mp4 pdf 2. Chowdhury, Nabil mp4 pdf	1. Jorgensen, W. L.; et al., Monte Carlo Simulation of Differences in Free Energies of Hydration. J. Chem. Phys. 1985, 83, 3050-3054 2. Still, W. C.; et al., Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. J. Am. Chem. Soc 1990, 112, 6127-6129	1. Thermodynamic Cycle as Drawn By Dr. Rizzo -
2021.09.27 Mon	Continuum Solvent Models 1. Poisson-Boltzmann Surface Area (PBSA) 2. Accuracy of partial atomic changes for GBSA and PBSA	1. Wen, Kangqiao mp4 pdf 2. Alcantara, Juan mp4 pdf	1. Sitkoff, D.; et al., Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. J. Phys. Chem. 1994, 98, 1978-1988 2. Rizzo, R. C.; et al., Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. J. Chem. Theory. Comput. 2006, 2, 128-139	-
-	-	-	Take home QUIZ for Section 2 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)	Additional resources: 1. Duarte Ramos Matos, G.; et al., Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database. J. Chem. Eng. Data 2017, 62, 1559-1569 2. Loeffler, H. H.; et al., Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages J. Chem. Theory Comput. 2018, 14, 5567−5582
2021.09.29 Wed	SECTION III: SAMPLING METHODS Molecular Conformations 1. Small molecules, peptides, relative energy, minimization methods Sampling Methods for Large Simulations 2. Molecular dynamics (MD)	1. Kochert, Matthew mp4 pdf 2. Genovese, Stacy mp4 pdf	1. Howard, A. E.; Kollman, P. A., An analysis of current methodologies for conformational searching of complex molecules. J. Med. Chem. 1988, 31, 1669-75 2. Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. Nature 1990, 347, 631-9	1. Section 4 (PAGES 22-27) Colby College Molecular Mechanics Tutorial Introduction, 2004, Shattuck, T.W., Colby College 1. Holloway, M. K., A priori prediction of ligand affinity by energy minimization. Perspect. Drug Discov. Design 1998, 9-11, 63-84
2021.10.04 Mon	Sampling Methods for Large Simulations 1. Monte Carlo (MC) Predicting Protein Structure 2. Ab initio structure prediction (protein-folding)	1. Jeon, Amy mp4 pdf 2. Dean, Noah mp4 pdf	1. Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B. 1. Jorgensen, W. L.; TiradoRives, J., Monte Carlo vs Molecular Dynamics for Conformational Sampling. J. Phys. Chem. 1996, 100,14508-14513 2. Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. Nat. Struct. Biol. 1997, 4, 10-19	1. Metropolis, N.;et al., Equation of State Calculations by Fast Computing Machines. The Journal of Chemical Physics 1953, 21, 1087-1092
2021.10.06 Wed	Predicting Protein Structure 1. Example Trp-cage 2. Comparative (homology) modeling	1. Ramcharan, Karishma mp4 pdf 2. Huang, Qiyao mp4 pdf	1. Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. J. Am. Chem. Soc. 2002, 124,11258-9 2. Marti-Renom, M. A.; et al., Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 2000,29,291-325	1. Daggett, V.; Fersht, A., The present view of the mechanism of protein folding. Nat. Rev. Mol. Cell Biol. 2003, 4, 497-502 2. Fiser, A.; et al., Evolution and physics in comparative protein structure modeling. Acc. Chem. Res. 2002, 35, 413-21
2021.10.11 Mon	No Class: Fall Break	-	-	-
2021.10.13 Wed	Predicting Protein Structure 1. Case studies (CASP) 2. Accelerated MD for Blind Protein Prediction	1. Song, Joon-Hyun mp4 pdf 2. Huffstutler, Thomas mp4 pdf	1. Moult, J., A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr. Opin. Struct. Biol. 2005,15, 285-9 2. Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. Sci. Adv. 2016, 2	1. Kryshtafovych, A.; et al., Progress over the first decade of CASP experiments. Proteins 2005, 61 Suppl 7, 225-36
2021.10.18 Mon	Predicting Protein Structure 1. Meso-Scale MD (Markov State Models) 2. Neural Networks	1. Paturu, Saigoutham mp4 pdf 2. Grange, Daniel mp4 pdf	1. Durrant, J.;et al, Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ACS Central Science 2020, 6, 189-196 2. Senior, A.;et al, Improved protein structure prediction using potentials from deep learning. Nature 2020, 577, 1-5	1. Husic, B.; et al., Markov State Models: From an Art to a Science. JACS 2018, 140, 2386-2396
-	-	-	Take home QUIZ for Section 3 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)	-
2021.10.20 Wed	SECTION IV: LEAD DISCOVERY Docking 1. Introduction to DOCK 2. Test Sets (database enrichment)	1. Liang, Heng mp4 pdf 2. Carter, Simon mp4 pdf	1. Allen, W. J.; et al., DOCK 6: Impact of New Features and Current Docking Performance. Journal of computational chemistry 2015, 36, 1132-1156. 2. Mysinger, M.; et al., Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. Journal of medicinal chemistry 2012, 55, 6582-94	1. Ewing, T. J.; et al., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J. Comput. Aided Mol. Des. 2001, 15, 411-28
2021.10.25 Mon	Docking 1. Test Sets (virtual screening) 2. Footprint-based scoring	1. Jiang, Yuhe mp4 pdf 2. Humphries, Kathryn mp4 pdf	1. Irwin, J. J.; Shoichet, B. K., ZINC--a free database of commercially available compounds for virtual screening. J. Chem. Inf. Model. 2005, 45, 177-82 2. Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. J. Comput. Chem. 2011, 32, 2273-2289.	1. ZINC Website at UCSF, Shoichet group
2021.10.27 Wed	Docking 1. GIST score Discovery Methods 2. Hotspot probes (GRID)	1. Feltman, Scott mp4 pdf 2. Boysan, Brock mp4 pdf	1. Balius, T.E.; et al., Testing inhomogeneous solvation theory in structure-based ligand discovery. Proceedings of the National Academy of Sciences 2017, 114, 201703287. 2. Goodford, P. J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 1985, 28, 849-57	1. Nguyen, C.; et al., Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. Journal of chemical theory and computation 2014, 10, 2769-2780.
2021.11.01 Mon	Discovery Methods 1. COMFA 2 Pharmacophores	1. Yearsley, Matthew mp4 pdf 2. Joshi, Anuja-Ria mp4 pdf	1. Kubinyi, H., Comparative molecular field analysis (CoMFA). Encyclopedia of Computational Chemistry, Databases and Expert Systems Section, John Wiley & Sons, Ltd. 1998 2. Chang, C.; et al., Pharmacophore-based discovery of ligands for drug transporters. Advanced Drug Delivery Reviews 2006, 58, 1431-1450	1. Cramer, R. D.; Patterson, D. E.; Bunce, J. D., Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc., 1988, 110, 5959-5967
2021.11.03 Wed	Discovery Methods. 1. Pharmacophores 2. De novo design	1. Delamonica, Brenda mp4 pdf 2. Chowdhury, Nabil mp4 pdf	1. Alvarez, J.; et al., Pharmacophore-Based Molecular Docking to Account for Ligand Flexibility. Proteins 2003, 51, 172-188 2. Cheron, N.; et al., OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. J. Med. Chem. 2016, 59, 4171-4188	-
2021.11.08 Mon	Discovery Methods 1. De novo design 2. Genetic Algorithm	1. Wen, Kangqiao mp4 pdf 2. Alcantara, Juan mp4 pdf	1. Jorgensen, W.; et al., Efficient drug lead discovery and optimization. Acc. of Chem. Research 2009, 42 (6), 724-733 2. Pegg, S. C.; Haresco, J. J.; Kuntz, I. D., A genetic algorithm for structure-based de novo design. J Comput Aided Mol Des 2001, 15, 911-33	-
-	-	-	Take home QUIZ for Section 4 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)	-
2021.11.010 Wed	SECTION V: LEAD REFINEMENT Free Energy Methods 1. Thermolysin with two ligands (FEP) 2. Fatty acid synthase I ligands (TI)	1. Kochert, Matthew mp4 pdf 2. Genovese, Stacy mp4 pdf	1. Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A., Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science 1987, 235, 574-6 2. Labahn, A.; et al., Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I. Bioorg Med Chem. 2012, 20, 3446-53	1&2. Jorgensen, W. L., Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution. Accounts Chem. Res. 1989, 22, 184-189 1&2. Kollman, P., Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. Chem. Rev. 1993, 93, 2395-2417 2. Lawrenz, M.; et al., Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. J. Chem. Theory Comput. 2009, 5, 1106-1116
2021.11.15 Mon	MM-PB/GBSA 1. Intro to Molecular Mechanics Poisson-Boltzmann / Generalized Born Surface Area Methods MM-GBSA case studies 2. EGFR and mutants	1. Jeon, Amy mp4 pdf 2. Dean, Noah mp4 pdf	1. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts Chem. Res. 2000, 33, 889-897 2. Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. Biochemistry, 2009, 48, 8435-8448
2021.11.17 Wed	MM-GBSA case studies 1. ErbB family selectivity Linear Response 2. Intro to Linear Response (LR method)	1. Ramcharan, Karishma mp4 pdf 2. Huang, Qiyao mp4 pdf	1. Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, Biochemistry, 2012, 51, 2390-2406 2. Aqvist, J.; Mowbray, S. L., Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations. J Biol Chem 1995, 270, 9978-81	-
2021.11.22 Mon	Linear Response 1. Inhibition of protein kinases (Extended LR method) Properties of Known Drugs 2. Molecular Scaffolds (frameworks) and functionality (side-chains	1. Song, Joon-Hyun mp4 pdf 2. Huffstutler, Thomas mp4 pdf	1. Tominaga, Y.; Jorgensen, W. L.; General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. J. Med. Chem. 2004, 47, 2534-2549 2. Bemis, G. W.; Murcko, M. A., The properties of known drugs. 1. Molecular frameworks. J. Med. Chem. 1996, 39, 2887-93 2. Bemis, G. W.; Murcko, M. A., Properties of known drugs. 2. Side chains. J. Med. Chem. 1999, 42, 5095-9	-
2021.11.24 Wed	No Class: Thanksgiving	-	-	-
2021.11.29 Mon	Properties of Known Drugs 1. Lipinski Rule of Five 2 ADME Prediction	1. Paturu, Saigoutham mp4 pdf 2. Grange, Daniel mp4 pdf	1. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug. Deliv. Rev. 2001, 46, 3-26 2. Hou, T. J.; Xu, X. J.; ADME evaluation in drug discovery. J. Mol. Model, 2002, 8, 337-349	1. Lipinski, C. A., Chris Lipinski discusses life and chemistry after the Rule of Five. Drug. Discov. Today 2003, 8, 12-6 2. Hou, T. J.; Xu, X. J.; AMDE Evaluation in drug discovery 3. Modeling blood-brain barrier partitioning using simple molecular descriptors. J. Chem. Inf. Comput. Sci., 2003, 43, 2137-2152
2021.12.01 Wed	Properties of Known Drugs 1. Synthetic Accessibility 2. QED	1. Liang, Heng mp4 pdf 2. Carter, Simon mp4 pdf	1. Ertl, P.; Schuffenhauer, A.; Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. J. Cheminformatics, 2009, 1, 8 2. Bickerton, G. R., Quantifying the chemical beauty of drugs. Nature Chemistry 2012, 4, 90-98	-
2021.12.06 Mon	From Target to Market 1. Drug Discovery Overview 2. Attrition Rates	1. Jiang, Yuhe mp4 pdf 2. Humphries, Kathryn mp4 pdf	1. Hughes, J.; et. al., Principles of early drug discovery. British journal of pharmacology 2010, 162, 1239-49. 2. Waring, M.; et. al., An analysis of the attrition of drug candidates from four major pharmaceutical companies Nature reviews 2015, 14.	2. Understanding Clinical Trial Terminology: What's a Phase 1, 2 OR 3 Clinical Trial?. www.concertpharma.com, 2019 Thermodynamic Cycles Course Wrap-Up Topics	-	-
-	-	-	Take home QUIZ for Section 5 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)	-
-	Final Exam	-	No Final Exam in AMS-535/CHE-535 for Fall 2020	-

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

Difference between revisions of "2021 AMS-535 Fall"

Latest revision as of 20:11, 3 December 2021

Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage

Online Syllabus Notes

Required Syllabi Statements:

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@@ Line 17: / Line 17: @@
 (1) Pre-recorded oral presentations (25%)
-::Student will pre-record 2 ZOOM presentations based on 2 papers assigned from the schedule below <br>
+::Student will pre-record 2 ZOOM presentations based on papers assigned from the schedule below <br>
 (2) Class discussion (30%)
 ::At scheduled class times students will be assigned into ZOOM breakout rooms and asked to discuss the papers they have read and the presentations they have watched <br>
@@ Line 44: / Line 44: @@
 '''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.
 == '''Online Syllabus Notes''' ==
@@ Line 61: / Line 60: @@
 '''Oral Presentations:'''
-*Students will pre-record 2 different ZOOM presentations based on 2 different papers from the schedule shown below.
+*Students will pre-record ZOOM presentations based on papers assigned to them from the schedule shown below.
 *Students will email their pre-recorded presentations to ALL course Instructors by Friday at 5PM before the week in which their presentations will be discussed.
 *Course participants will watch the student presentations before the class in which they are to be discussed.
@@ Line 105: / Line 104: @@
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-| <center>2020.08.24 Mon</center>
+| <center>2021.08.23 Mon</center>
 ||
 *''Organizational Meeting
-||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.08.24.ams535.rizzo.organizational.mp4 Rizzo, R. mp4]
+||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.08.23.ams535.rizzo.organizational.mp4 Rizzo, R. mp4]
 || Course introduction and format.  Go over Syllabus.  Course participant background and introductions.
 || <center>-</center>
 |-
-| <center>2020.08.26 Wed</center>
+| <center>2021.08.25 Wed</center>
 ||
 '''SECTION I: DRUG DISCOVERY AND BIOMOLECULAR STRUCTURE'''
@@ Line 121: / Line 120: @@
 ||
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.08.26.ams535.rizzo.lect.001.mp4 Rizzo, R. mp4]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.08.25.ams535.rizzo.lect.001.mp4 Rizzo, R. mp4]
 <br>
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.08.26.ams535.rizzo.lect.001.pdf Rizzo, R. pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.08.25.ams535.rizzo.lect.001.pdf Rizzo, R. pdf]
 ||
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen009.pdf Jorgensen, W.L., The many roles of computation in drug discovery. ''Science'' '''2004''', ''303'', 1813-8]
@@ Line 132: / Line 131: @@
 |-
-| <center>2020.08.31 Mon</center>
+| <center>2021.08.30 Mon</center>
 ||
 *''Chemistry Review''
@@ Line 139: / Line 138: @@
 ||
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.08.31.ams535.rizzo.lect.002.mp4 Rizzo, R. mp4]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.08.30.ams535.rizzo.lect.002.mp4 Rizzo, R. mp4]
 <br>
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.08.31.ams535.rizzo.lect.002.pdf Rizzo, R. pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.08.30.ams535.rizzo.lect.002.pdf Rizzo, R. pdf]
 || <center>presentation</center>
 || <center>-</center>
 |-
-| <center>2020.09.02 Wed</center>
+| <center>2021.09.01 Wed</center>
 ||
 *''Biomolecular Structure''
@@ Line 154: / Line 153: @@
 ||
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.02.ams535.rizzo.lect.003.mp4 Rizzo, R. mp4]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.01.ams535.rizzo.lect.003.mp4 Rizzo, R. mp4]
 <br>
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.02.ams535.rizzo.lect.003.pdf Rizzo, R. pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.01.ams535.rizzo.lect.003.pdf Rizzo, R. pdf]
 || <center>presentation</center>
 || [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/2010.amino_acids_scanned.pdf structures of the 20 amino acid side chains]
@@ Line 163: / Line 162: @@
 |- style="background:peachpuff"
-| <center>2020.09.07 Mon</center>
+| <center>2021.09.06 Mon</center>
 ||
 *''No Class: Labor Day''
@@ Line 171: / Line 170: @@
 |-
-| <center>2020.09.09 Wed</center>
+| <center>2021.09.08 Wed</center>
 ||
 *''Molecular Interactions and Recognition''
@@ Line 177: / Line 176: @@
 :2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive
 ||
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.09.ams535.rizzo.lect.004.mp4 Rizzo, R. mp4]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.08.ams535.rizzo.lect.004.mp4 Rizzo, R. mp4]
 <br>
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.09.ams535.rizzo.lect.004.pdf Rizzo, R. pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.08.ams535.rizzo.lect.004.pdf Rizzo, R. pdf]
 || <center>presentation</center>
 || <center>-</center>
 |-
-| <center>2020.09.14 Mon</center>
+| <center>2021.09.13 Mon</center>
 ||
 *''Intro. to Methods in 3-D Structure Determination''
@@ Line 191: / Line 190: @@
 :2. Structure Quality, PDB in detail
 ||
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.14.ams535.rizzo.lect.005.mp4 Rizzo, R. mp4]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.13.ams535.rizzo.lect.005.mp4 Rizzo, R. mp4]
 <br>
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.14.ams535.rizzo.lect.005.pdf Rizzo, R. pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.13.ams535.rizzo.lect.005.pdf Rizzo, R. pdf]
 || <center>presentation</center>
 || <center>-</center>
@@ Line 207: / Line 206: @@
 |-
-| <center>2020.09.16 Wed </center>
+| <center>2021.09.15 Wed </center>
 ||
 '''SECTION II: MOLECULAR MODELING'''
@@ Line 215: / Line 214: @@
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.16.AMS535.talk01.mp4 Adams, Dexter mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.15.AMS535.talk01.mp4 Feltman, Scott mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.16.AMS535.talk01.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.15.AMS535.talk01.pdf  pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.16.AMS535.talk02.mp4 Chang, Jamie mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.15.AMS535.talk02.mp4 Boysan, Brock mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.16.AMS535.talk02.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.15.AMS535.talk02.pdf  pdf]
 ||
@@ Line 235: / Line 234: @@
 |-
-| <center>2020.09.21 Mon</center>
+| <center>2021.09.20 Mon</center>
 ||
 *''Classical Force Fields''
@@ Line 243: / Line 242: @@
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.21.AMS535.talk01.mp4 Corbo, Chris mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.20.AMS535.talk01.mp4 Yearsley, Matthew mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.21.AMS535.talk01.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.20.AMS535.talk01.pdf  pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.21.AMS535.talk02.mp4 Chung, So Young mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.20.AMS535.talk02.mp4 Joshi, Anuja-Ria mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.21.AMS535.talk02.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.20.AMS535.talk02.pdf  pdf]
 ||
@@ Line 260: / Line 259: @@
 |-
-| <center>2020.09.23 Wed </center>
+| <center>2021.09.22 Wed </center>
 ||
 *''Explicit Solvent Models''
@@ Line 268: / Line 267: @@
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.23.AMS535.talk01.mp4  Dovedytis, Matt mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.22.AMS535.talk01.mp4  Delamonica, Brenda mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.23.AMS535.talk01.pdf   pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.22.AMS535.talk01.pdf   pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.23.AMS535.talk02.mp4  Foran, Chris mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.22.AMS535.talk02.mp4  Chowdhury, Nabil mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.23.AMS535.talk02.pdf   pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.22.AMS535.talk02.pdf   pdf]
 ||
@@ Line 282: / Line 281: @@
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Still001.pdf Still, W. C.; et al., Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. ''J. Am. Chem. Soc'' 1990, ''112'', 6127-6129]
 ||
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/DDGhyd_cycle.pdf Thermodynamic Cycle as Drawn By Dr. Rizzo]
 <center>-</center>
 |-
-| <center>2020.09.28 Mon</center>
+| <center>2021.09.27 Mon</center>
 ||
 *''Continuum Solvent Models''
@@ Line 292: / Line 294: @@
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.28.AMS535.talk01.mp4  Hall, Carole mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.27.AMS535.talk01.mp4  Wen, Kangqiao mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.28.AMS535.talk01.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.27.AMS535.talk01.pdf  pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.28.AMS535.talk02_2.mp4  Lang, Liam mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.27.AMS535.talk02.mp4  Alcantara, Juan mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.28.AMS535.talk02.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.27.AMS535.talk02.pdf  pdf]
 ||
@@ Line 318: / Line 320: @@
 |-
-| <center>2020.09.30 Wed </center>
+| <center>2021.09.29 Wed </center>
 ||
 '''SECTION III: SAMPLING METHODS'''
@@ Line 327: / Line 329: @@
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.30.AMS535.talk01.mp4  Mingione, Victoria mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.29.AMS535.talk01.mp4  Kochert, Matthew mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.30.AMS535.talk01.pdf   pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.29.AMS535.talk01.pdf   pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.30.AMS535.talk02.mp4 Palmeri, Chris mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.29.AMS535.talk02.mp4 Genovese, Stacy mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.30.AMS535.talk02.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.29.AMS535.talk02.pdf  pdf]
 ||
@@ Line 346: / Line 348: @@
 |-
-| <center>2020.10.05 Mon </center>
+| <center>2021.10.04 Mon </center>
 ||
 *''Sampling Methods for Large Simulations''
@@ Line 354: / Line 356: @@
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.05.AMS535.talk01.mp4 Pasumarthy, Sishir mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.04.AMS535.talk01.mp4 Jeon, Amy mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.05.AMS535.talk01.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.04.AMS535.talk01.pdf  pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.05.AMS535.talk02.mp4 Quispe-Carbajal, Mariella mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.04.AMS535.talk02.mp4 Dean, Noah mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.05.AMS535.talk02.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.04.AMS535.talk02.pdf  pdf]
 ||
@@ Line 373: / Line 375: @@
 |-
-| <center>2020.10.07 Wed </center>
+| <center>2021.10.06 Wed </center>
 ||
 *''Predicting Protein Structure''
@@ Line 380: / Line 382: @@
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.07.AMS535.talk01.mov  Rajesh, Chandana mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.06.AMS535.talk01.mp4  Ramcharan, Karishma mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.07.AMS535.talk01.pdf   pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.06.AMS535.talk01.pdf   pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.07.AMS535.talk02.mp4  Rangwala, Aziz mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.06.AMS535.talk02.mp4  Huang, Qiyao mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.07.AMS535.talk02.pdf   pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.06.AMS535.talk02.pdf   pdf]
 ||
@@ Line 399: / Line 401: @@
 |-
-| <center>2020.10.12 Mon</center>
+|- style="background:peachpuff"
+| <center>2021.10.11 Mon</center>
+||
+*''No Class: Fall Break''
+||<center>-</center>
+||<center>-</center>
+||<center>-</center>
+|-
+| <center>2021.10.13 Wed</center>
 ||
 *''Predicting Protein Structure''
@@ Line 405: / Line 417: @@
 :2. Accelerated MD for Blind Protein Prediction
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.12.AMS535.talk01.mp4 Sadatrezaei, Golbahar mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.13.AMS535.talk01.mp4 Song, Joon-Hyun mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.12.AMS535.talk01.pdf   pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.13.AMS535.talk01.pdf   pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.12.AMS535.talk02.mp4 Steier, Joshua mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.13.AMS535.talk02.mp4 Huffstutler, Thomas mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.12.AMS535.talk02.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.13.AMS535.talk02.pdf  pdf]
 ||
@@ Line 423: / Line 435: @@
 |-
-| <center>2020.10.14 Wed</center>
+| <center>2021.10.18 Mon</center>
 ||
 *''Predicting Protein Structure''
-:1. MD x-ray refinement
+:1. Meso-Scale MD (Markov State Models)
-:2. Protein Design
+:2. Neural Networks
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.14.AMS535.talk01.mp4 Contorno, Shaymus mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.18.AMS535.talk01.mp4 Paturu, Saigoutham mp4 ]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.14.AMS535.talk01.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.18.AMS535.talk01.pdf  pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.14.AMS535.talk02.mp4 He, Yongle mp4 ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.18.AMS535.talk02.mp4 Grange, Daniel mp4 ]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.14.AMS535.talk02.pdf   pdf ]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.18.AMS535.talk02.pdf   pdf ]
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Brunger001.pdf Brunger, A. T.;Adams, P. D., Molecular dynamics applied to X-ray structure refinement. ''Acc. Chem. Res.'' '''2002''', ''35'', 404-12]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Amaro001.pdf Durrant, J.;et al, Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ''ACS Central Science'' '''2020''', ''6'', 189-196]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Baker001.pdf Kuhlman, A. T.;et al, Design of a Novel Globular Protein Fold with Atomic-Level Accuracy. ''Science'' '''2003''', ''302'', 1364-1368]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Hassabis001.pdf Senior, A.;et al, Improved protein structure prediction using potentials from deep learning. ''Nature'' '''2020''', ''577'', 1-5]
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Brunger004.pdf Adams, P. D.; et al., Extending the limits of molecular replacement through combined simulated annealing and maximum-likelihood refinement. ''Acta Crystallogr D Biol Crystallogr'' '''1999''', ''55'', 181-90]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pande002.pdf Husic, B.; et al., Markov State Models: From an Art to a Science. ''JACS'' '''2018''', ''140'', 2386-2396]
 |-
@@ Line 457: / Line 470: @@
 |-
-| <center>2020.10.19 Mon </center>
+| <center>2021.10.20 Wed </center>
 ||
 '''SECTION IV: LEAD DISCOVERY'''
 *''Docking''
 :1. Introduction to DOCK
-:2. Test Sets (pose reproduction)
+:2. Test Sets (database enrichment)
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.19.AMS535.talk01.mp4 Hetherington, Caitlin mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.20.AMS535.talk01.mp4 Liang, Heng mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.19.AMS535.talk01.pdf   pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.20.AMS535.talk01.pdf   pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.19.AMS535.talk02.mp4 Koller, Angus mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.20.AMS535.talk02.mp4 Carter, Simon mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.19.AMS535.talk02.pdf   pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.20.AMS535.talk02.pdf   pdf]
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo014.pdf Moustakas, D. T.; et al., Development and Validation of a Modular, Extensible Docking program: DOCK 5. ''J. Comput. Aided Mol. Des.'' '''2006''', ''20'', 601-619]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo035.pdf Allen, W. J.; et al., DOCK 6: Impact of New Features and Current Docking Performance. ''Journal of computational chemistry'' '''2015''', ''36'', 1132-1156.]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo021.pdf Mukherjee, S.; et al., Docking Validation Resources: Protein Family and Ligand Flexibility Experiments. ''J. Chem. Info. Model.'' '''2010''', ''50'', 1986-2000]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet003.pdf Mysinger, M.; et al., Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. ''Journal of medicinal chemistry'' '''2012''', ''55'', 6582-94]
 ||
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz002.pdf Ewing, T. J.; et al., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. ''J. Comput. Aided Mol. Des.'' '''2001''', ''15'', 411-28]
-. [http://www.ccdc.cam.ac.uk/products/life_sciences/gold/validation/astex/ The CCDC/Astex Test Set]
 |-
-| <center>2020.10.21 Wed</center>
+| <center>2021.10.25 Mon</center>
 ||
 *''Docking''
 :1. Test Sets (virtual screening)
-:2. Test Sets (database enrichment)
+:2. Footprint-based scoring
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.21.AMS535.talk01.mp4 Pak, Steven mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.25.AMS535.talk01.mp4 Jiang, Yuhe mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.21.AMS535.talk01.pdf   pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.25.AMS535.talk01.pdf   pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.21.AMS535.talk02.mp4 Adams, Dexter mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.25.AMS535.talk02.mp4 Humphries, Kathryn mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.21.AMS535.talk02.pdf   pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.25.AMS535.talk02.pdf   pdf]
 ||
@@ Line 504: / Line 516: @@
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet001.pdf Irwin, J. J.; Shoichet, B. K., ZINC--a free database of commercially available compounds for virtual screening. ''J. Chem. Inf. Model.'' '''2005''', ''45'', 177-82]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet002.pdf Huang, N.; et al., Benchmarking Sets for Molecular Docking. ''J. Med. Chem.'' '''2006''', ''49(23)'', 6789-6801]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo022.pdf Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. ''J. Comput. Chem.'' '''2011''', ''32'', 2273-2289.]
 ||
@@ Line 511: / Line 523: @@
 |-
-| <center>2020.10.26 Mon</center>
+| <center>2021.10.27 Wed</center>
 ||
 *''Docking''
-:1. Footprint-based scoring
+:1. GIST score
 *''Discovery Methods''
 :2. Hotspot probes (GRID)
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.26.AMS535.talk01.mp4 Chang, Jaime mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.27.AMS535.talk01.mp4 Feltman, Scott mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.26.AMS535.talk01.pdf   pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.27.AMS535.talk01.pdf   pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.26.AMS535.talk02.mp4 Corbo, Chris mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.27.AMS535.talk02.mp4 Boysan, Brock mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.26.AMS535.talk02.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.10.27.AMS535.talk02.pdf  pdf]
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo022.pdf Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. ''J. Comput. Chem.'' '''2011''', ''32'', 2273-2289.]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet004.pdf Balius, T.E.; et al., Testing inhomogeneous solvation theory in structure-based ligand discovery. ''Proceedings of the National Academy of Sciences'' '''2017''', ''114'', 201703287.]
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Goodford001.pdf Goodford, P. J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. ''J. Med. Chem.'' '''1985''', ''28'', 849-57]
 ||
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kurtzman001.pdf Nguyen, C.; et al., Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. ''Journal of chemical theory and computation'' '''2014''', ''10'', 2769-2780.]
+|-
 <center>-</center>
 |-
-| <center>2020.10.28 Wed</center>
+| <center>2021.11.01 Mon</center>
 ||
 *''Discovery Methods''
@@ Line 543: / Line 559: @@
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.28.AMS535.talk01.mp4 Chung, So Young mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.01.AMS535.talk01.mp4 Yearsley, Matthew mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.28.AMS535.talk01.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.01.AMS535.talk01.pdf  pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.28.AMS535.talk02.mp4 Dovedytis, Matt mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.01.AMS535.talk02.mp4 Joshi, Anuja-Ria mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.28.AMS535.talk02.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.01.AMS535.talk02.pdf  pdf]
 ||
@@ Line 560: / Line 576: @@
 |-
-| <center>2020.11.02 Mon</center>
+| <center>2021.11.03 Wed</center>
 ||
 *''Discovery Methods.''
@@ Line 567: / Line 583: @@
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.02.AMS535.talk01.mp4 Foran, Chris mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.03.AMS535.talk01.mp4 Delamonica, Brenda mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.02.AMS535.talk01.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.03.AMS535.talk01.pdf  pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.02.AMS535.talk02.mp4 Hall, Carole mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.03.AMS535.talk02.mp4 Chowdhury, Nabil mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.02.AMS535.talk02.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.03.AMS535.talk02.pdf  pdf]
 ||
@@ Line 582: / Line 598: @@
 |-
-| <center>2020.11.04 Wed</center>
+| <center>2021.11.08 Mon</center>
 ||
 *''Discovery Methods''
@@ Line 589: / Line 605: @@
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.04.AMS535.talk01.mp4 Lang, Liam mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.08.AMS535.talk01.mp4 Wen, Kangqiao mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.04.AMS535.talk01.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.08.AMS535.talk01.pdf  pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.04.AMS535.talk02.mp4 Mingione, Victoria mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.08.AMS535.talk02.mp4 Alcantara, Juan mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.04.AMS535.talk02.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.08.AMS535.talk02.pdf  pdf]
 ||
@@ Line 612: / Line 628: @@
 |-
-| <center>2020.11.09 Mon</center>
+| <center>2021.11.010 Wed</center>
 ||
 '''SECTION V: LEAD REFINEMENT
@@ Line 620: / Line 636: @@
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.09.AMS535.talk01.mp4  Palmeri, Chris mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.10.AMS535.talk01.mp4  Kochert, Matthew mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.09.AMS535.talk01.pdf   pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.10.AMS535.talk01.pdf   pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.09.AMS535.talk02.mp4  Pasumarthy, Sishir mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.10.AMS535.talk02.mp4  Genovese, Stacy mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.09.AMS535.talk02.pdf   pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.10.AMS535.talk02.pdf   pdf]
 ||
@@ Line 641: / Line 657: @@
 |-
-| <center>2020.11.11 Wed</center>
+| <center>2021.11.15 Mon</center>
 ||
@@ Line 650: / Line 666: @@
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.11.AMS535.talk01.mp4  Quispe-Carbajal, Mariella  mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.15.AMS535.talk01.mp4  Jeon, Amy mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.11.AMS535.talk01.pdf   pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.15.AMS535.talk01.pdf   pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.11.AMS535.talk02.mp4  Rajesh, Chandana  mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.15.AMS535.talk02.mp4  Dean, Noah mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.11.AMS535.talk02.pdf   pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.15.AMS535.talk02.pdf   pdf]
 ||
@@ Line 667: / Line 683: @@
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-| <center>2020.11.16 Mon </center>
+| <center>2021.11.17 Wed </center>
 ||
 *''MM-GBSA case studies''
@@ Line 675: / Line 691: @@
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.16.AMS535.talk01.mp4 Rangwala, Aziz mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.17.AMS535.talk01.mp4 Ramcharan, Karishma mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.16.AMS535.talk01.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.17.AMS535.talk01.pdf  pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.16.AMS535.talk02.mp4 Sadatrezaei, Golbahar mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.17.AMS535.talk02.mp4 Huang, Qiyao mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.16.AMS535.talk02.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.17.AMS535.talk02.pdf  pdf]
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@@ Line 693: / Line 709: @@
 |-
-| <center>2020.11.18 Wed </center>
+| <center>2021.11.22 Mon </center>
 ||
 *''Linear Response''
@@ Line 701: / Line 717: @@
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.18.AMS535.talk01.mp4  Steier, Joshua mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.22.AMS535.talk01.mp4  Song, Joon-Hyun mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.18.AMS535.talk01.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.22.AMS535.talk01.pdf  pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.18.AMS535.talk02.mp4  Contorno, Shaymus mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.22.AMS535.talk02.mp4  Huffstutler, Thomas mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.18.AMS535.talk02.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.22.AMS535.talk02.pdf  pdf]
 ||
@@ Line 717: / Line 733: @@
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko002.pdf Bemis, G. W.; Murcko, M. A., Properties of known drugs. 2. Side chains. ''J. Med. Chem.'' '''1999''', ''42'', 5095-9]
-||<center>-</center>
-|-
-|- style="background:peachpuff"
-| <center>2020.11.23 Mon</center>
-||
-*''No Class: Thanksgiving''
-||<center>-</center>
-||<center>-</center>
 ||<center>-</center>
 |-
 |- style="background:peachpuff"
-| <center>2020.11.25 Wed</center>
+| <center>2021.11.24 Wed</center>
 ||
 *''No Class: Thanksgiving''
@@ Line 737: / Line 744: @@
 |-
-| <center>2020.11.30 Mon </center>
+| <center>2021.11.29 Mon </center>
 ||
 *''Properties of Known Drugs''
@@ Line 744: / Line 751: @@
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.AMS535.talk01.mp4  He, Yongle mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.29.AMS535.talk01.mp4  Paturu, Saigoutham mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.AMS535.talk01.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.29.AMS535.talk01.pdf  pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.AMS535.talk02.mp4   Hetherington, Caitlin mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.29.AMS535.talk02.mp4   Grange, Daniel mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.AMS535.talk02.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.11.29.AMS535.talk02.pdf  pdf]
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@@ Line 764: / Line 771: @@
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-| <center>2020.12.02 Wed </center>
+| <center>2021.12.01 Wed </center>
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 *''Properties of Known Drugs''
@@ Line 770: / Line 777: @@
 :2. QED
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.12.02.AMS535.talk01.mp4  Koller, Angus mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.12.01.AMS535.talk01.mp4  Liang, Heng mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.12.02.AMS535.talk01.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.12.01.AMS535.talk01.pdf  pdf]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.12.02.AMS535.talk02.mp4   Pak, Steve mp4]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.12.01.AMS535.talk02.mp4   Carter, Simon mp4]
 <br>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.12.02.AMS535.talk02.pdf  pdf]
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.12.01.AMS535.talk02.pdf  pdf]
 ||
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Ertl2009.pdf Ertl, P.; Schuffenhauer, A.; Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions. ''J. Cheminformatics'', '''2009''', ''1'', 8]
@@ Line 784: / Line 791: @@
 |-
-| <center>2020.12.07 Mon </center>
+| <center>2021.12.06 Mon </center>
 ||
-* Course Wrap-up
+*''From Target to Market''
-||<center>[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535_thermo_cycles_study_guide.pdf Thermodynamic Cycles]
+:1. Drug Discovery Overview
+:2. Attrition Rates
+||
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.12.06.AMS535.talk01.mp4  Jiang, Yuhe mp4]
+<br>
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.12.06.AMS535.talk01.pdf  pdf]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.12.06.AMS535.talk02.mp4   Humphries, Kathryn mp4]
+<br>
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.12.06.AMS535.talk02.pdf  pdf]
+||
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Philpott001.pdf Hughes, J.;  et. al., Principles of early drug discovery. ''British journal of pharmacology'' '''2010''', ''162'', 1239-49.]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Weir001.pdf Waring, M.; et. al., An analysis of the attrition of drug candidates from four major pharmaceutical companies ''Nature reviews'' '''2015''', ''14''.]
+||<center>
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/ClinicalTrials.pdf Understanding Clinical Trial Terminology: What's a Phase 1, 2 OR 3 Clinical Trial?. ''www.concertpharma.com'', '''2019''']
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535_thermo_cycles_study_guide.pdf Thermodynamic Cycles]
+<br>
 [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535.course_topic_wrapup.pdf Course Wrap-Up Topics]
 </center>
@@ Line 821: / Line 845: @@
-'''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 University Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Faculty in the HSC Schools and the School of Medicine are required to follow their school-specific procedures. Further information about most academic matters can be found in the Undergraduate Bulletin, the Undergraduate Class Schedule, and the Faculty-Employee Handbook.
+'''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