Difference between revisions of "2020 AMS-535 Fall"

Latest revision as of 18:17, 8 September 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] Dr. Guilherme Duarte Ramos Matos [631-632-8519, guilherme dot duarteramosmatos -at- stonybrook dot edu] John Bickel [631-632-8519, john dot bickel -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 2 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 2 different ZOOM presentations based on 2 different papers 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
2020.08.24 Mon	Organizational Meeting	Rizzo, R. mp4	Course introduction and format. Go over Syllabus. Course participant background and introductions.	-
2020.08.26 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	-
2020.08.31 Mon	Chemistry Review 1. Molecular structure, bonding, graphical representations 2. Functionality, properties of organic molecules	Rizzo, R. mp4 Rizzo, R. pdf	presentation	-
2020.09.02 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
2020.09.07 Mon	No Class: Labor Day	-	-	-
2020.09.09 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	-
2020.09.14 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)	-
2020.09.16 Wed	SECTION II: MOLECULAR MODELING Classical Force Fields 1. All-atom Molecular Mechanics 2. OPLS	1. Adams, Dexter mp4 pdf 2. Chang, Jamie 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
2020.09.21 Mon	Classical Force Fields 1. AMBER Explicit Solvent Models 2. Water models (TIP3P, TIP4P, SPC)	1. Corbo, Chris mp4 pdf 2. Chung, So Young 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
2020.09.23 Wed	Explicit Solvent Models 1. Condensed-phase calculations (DGhydration) Continuum Solvent Models 2. Generalized Born Surface Area (GBSA)	1. Dovedytis, Matt mp4 pdf 2. Foran, Chris 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	-
2020.09.28 Mon	Continuum Solvent Models 1. Poisson-Boltzmann Surface Area (PBSA) 2. Accuracy of partial atomic changes for GBSA and PBSA	1. Hall, Carole mp4 pdf 2. Lang, Liam 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
2020.09.30 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. Mingione, Victoria mp4 pdf 2. Palmeri, Chris 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
2020.10.05 Mon	Sampling Methods for Large Simulations 1. Monte Carlo (MC) Predicting Protein Structure 2. Ab initio structure prediction (protein-folding)	1. Pasumarthy, Sishir mp4 pdf 2. Quispe-Carbajal, Mariella 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
2020.10.07 Wed	Predicting Protein Structure 1. Example Trp-cage 2. Comparative (homology) modeling	1. Rajesh, Chandana mp4 pdf 2. Rangwala, Aziz 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
2020.10.12 Mon	Predicting Protein Structure 1. Case studies (CASP) 2. Accelerated MD for Blind Protein Prediction	1. Sadatrezaei, Golbahar mp4 pdf 2. Steier, Joshua 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
2020.10.14 Wed	Predicting Protein Structure 1. MD x-ray refinement 2. Protein Design	1. Contorno, Shaymus mp4 pdf 2. He, Yongle mp4 pdf	1. Brunger, A. T.;Adams, P. D., Molecular dynamics applied to X-ray structure refinement. Acc. Chem. Res. 2002, 35, 404-12 2. Kuhlman, A. T.;et al, Design of a Novel Globular Protein Fold with Atomic-Level Accuracy. Science 2003, 302, 1364-1368	1. 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
-	-	-	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)	-
2020.10.19 Mon	SECTION IV: LEAD DISCOVERY Docking 1. Introduction to DOCK 2. Test Sets (pose reproduction)	1. Hetherington, Caitlin mp4 pdf 2. Koller, Angus mp4 pdf	1. 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 2. Mukherjee, S.; et al., Docking Validation Resources: Protein Family and Ligand Flexibility Experiments. J. Chem. Info. Model. 2010, 50, 1986-2000	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 2. The CCDC/Astex Test Set
2020.10.21 Wed	Docking 1. Test Sets (virtual screening) 2. Test Sets (database enrichment)	1. Pak, Steven mp4 pdf 2. Adams, Dexter 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. Huang, N.; et al., Benchmarking Sets for Molecular Docking. J. Med. Chem. 2006, 49(23), 6789-6801	1. ZINC Website at UCSF, Shoichet group
2020.10.26 Mon	Docking 1. Footprint-based scoring Discovery Methods 2. Hotspot probes (GRID)	1. Chang, Jaime mp4 pdf 2. Corbo, Chris mp4 pdf	1. Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. J. Comput. Chem. 2011, 32, 2273-2289. 2. Goodford, P. J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 1985, 28, 849-57	-
2020.10.28 Wed	Discovery Methods 1. COMFA 2 Pharmacophores	1. Chung, So Young mp4 pdf 2. Dovedytis, Matt 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
2020.11.02 Mon	Discovery Methods. 1. Pharmacophores 2. De novo design	1. Foran, Chris mp4 pdf 2. Hall, Carole 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	-
2020.11.04 Wed	Discovery Methods 1. De novo design 2. Genetic Algorithm	1. Lang, Liam mp4 pdf 2. Mingione, Victoria 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)	-
2020.11.09 Mon	SECTION V: LEAD REFINEMENT Free Energy Methods 1. Thermolysin with two ligands (FEP) 2. Fatty acid synthase I ligands (TI)	1. Palmeri, Chris mp4 pdf 2. Pasumarthy, Sishir 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
2020.11.11 Wed	MM-PB/GBSA 1. Intro to Molecular Mechanics Poisson-Boltzmann / Generalized Born Surface Area Methods MM-GBSA case studies 2. EGFR and mutants	1. Quispe-Carbajal, Mariella mp4 pdf 2. Rajesh, Chandana 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
2020.11.16 Mon	MM-GBSA case studies 1. ErbB family selectivity Linear Response 2. Intro to Linear Response (LR method)	1. Rangwala, Aziz mp4 pdf 2. Sadatrezaei, Golbahar 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	-
2020.11.18 Wed	Linear Response 1. Inhibition of protein kinases (Extended LR method) Properties of Known Drugs 2. Molecular Scaffolds (frameworks) and functionality (side-chains	1. Steier, Joshua mp4 pdf 2. Contorno, Shaymus 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	-
2020.11.23 Mon	No Class: Thanksgiving	-	-	-
2020.11.25 Wed	No Class: Thanksgiving	-	-	-
2020.11.30 Mon	Properties of Known Drugs 1. Lipinski Rule of Five 2 ADME Prediction	1. He, Yongle mp4 pdf 2. Hetherington, Caitlin 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
2020.12.02 Wed	Properties of Known Drugs 1. Synthetic Accessibility 2. QED	1. Koller, Angus mp4 pdf 2. Pak, Steve 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	-
2020.12.07 Mon	Course Wrap up	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 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.

Difference between revisions of "2020 AMS-535 Fall"

Latest revision as of 18:17, 8 September 2021

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

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@@ Line 5: / Line 5: @@
 ! style="width:10%" | '''Instructor'''
 | Dr. Robert C. Rizzo    [631-632-8519, rizzorc -at- gmail.com]
-|-
-|'''TA'''
+Dr. Guilherme Duarte Ramos Matos [631-632-8519, guilherme dot duarteramosmatos -at- stonybrook dot edu]
-|  Dr. Guilherme Duarte Ramos Matos [631-632-8519, guilherme dot duarteramosmatos -at- stonybrook dot edu]
 John Bickel  [631-632-8519, john dot bickel -at- stonybrook dot edu]
@@ Line 16: / Line 15: @@
 |-
 | '''Office Hours''' || Anytime by appointment, Math Tower 3-129
+|-
+| '''Grading''' ||  Grades will be based on the quality of: <br>
+(1) Pre-recorded oral presentations (25%)
+::Student will pre-record 2 ZOOM presentations based on 2 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>
+(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
 |-
 |}
+<br>
+'''GENERAL INFORMATION:''' AMS-535 provides an introduction to the field of computational structure-based drug design. The course aims to foster collaborative learning and will consist of presentations by instructors, course participants, and guest lecturers arranged in five major sections outlined below. Presentations should aim to summarize key papers, theory, and application of computational methods relevant to computational drug design. Grade will be based on 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: <br />Drug Discovery, Chemistry Review, Proteins, Carbohydrates, Nucleic acids <br />Molecular Interactions and Recognition, Experimental Techniques for Elucidating Structure
+**(ii) Molecular Modeling: <br />Classical Force Fields (Molecular Mechanics),  <br />Solvent Models, Condensed-phase Calculations, Parameter Development
+**(iii) Sampling Methods: <br />Conformational Space, Molecular Dynamics (MD), Metropolis Monte Carlo (MC) <br />Sampling Techniques, Predicting Protein Structure, Protein Folding
+**(iv) Lead Discovery:<br />Docking as a Lead Generation Tool, Docking Algorithms<br />Discovery Methods I, Discovery Methods II, Applications
+**(v) Lead Refinement:<br />Free Energy Perturbation (FEP), Linear Response (LR), Extended Linear Response (ELR)<br />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 [https://it.stonybrook.edu/services/zoom 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  [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.paper.summary.docx Paper Summary Sheet] answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Discussion" part of their grade for any synchronous classes that were missed.
+*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 2 different ZOOM presentations based on 2 different papers 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 [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.presentation.assessment.docx Presentation Assessment Sheet] which will be emailed to ALL Instructors within 24 hours after the class in which the presentation were discussed.
+'''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
+<br>
 <br>
@@ Line 29: / Line 107: @@
 |-
+| <center>2020.08.24 Mon</center>
-| <center>2019.08.24 Mon</center>
 ||
 *''Organizational Meeting
-|| <center>-</center>
+||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.08.24.ams535.rizzo.organizational.mp4 Rizzo, R. mp4]
-|| <center>-</center>
+|| Course introduction and format.  Go over Syllabus.  Course participant background and introductions.
 || <center>-</center>
 |-
+| <center>2020.08.26 Wed</center>
-| <center>2019.08.26 Wed</center>
 ||
 '''SECTION I: DRUG DISCOVERY AND BIOMOLECULAR STRUCTURE'''
+*''Drug Discovery''
+:1. Introduction, history, irrational vs. rational
+:2. Viral Target Examples
-*''Drug Discovery''
+||
-#Introduction, history, irrational vs. rational
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.08.26.ams535.rizzo.lect.001.mp4 Rizzo, R. mp4]
-#Viral Target Examples
+<br>
-||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.08.28.ams535.rizzo.lect.001.pdf Rizzo, R.]
+<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/References/Jorgensen009.pdf Jorgensen, W.L., The many roles of computation in drug discovery. ''Science'' '''2004''', ''303'', 1813-8]
@@ Line 53: / Line 133: @@
 || <center>-</center>
 |-
-| <center>2019.08.31 Mon</center>
+| <center>2020.08.31 Mon</center>
 ||
 *''Chemistry Review''
-#Molecular structure, bonding, graphical representations
+:1. Molecular structure, bonding, graphical representations
-#Functionality, properties of organic molecules
+:2. Functionality, properties of organic molecules
-||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.09.04.ams535.rizzo.lect.002.pdf Rizzo, R.]
+||
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.08.31.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]
 || <center>presentation</center>
 || <center>-</center>
 |-
-| <center>2019.09.02 Wed</center>
+| <center>2020.09.02 Wed</center>
 ||
 *''Biomolecular Structure''
-#Lipids, carbohydrates
+:1. Lipids, carbohydrates
-#Nucleic acids, proteins
+:2. Nucleic acids, proteins
-||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.09.9.ams535.rizzo.lect.003.pdf Rizzo, R.]
+||
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.02.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]
 || <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 74: / Line 165: @@
 |- style="background:peachpuff"
-| <center>2019.09.07 Mon</center>
+| <center>2020.09.07 Mon</center>
 ||
 *''No Class: Labor Day''
@@ Line 82: / Line 173: @@
 |-
-| <center>2019.09.09 Wed</center>
+| <center>2020.09.09 Wed</center>
 ||
 *''Molecular Interactions and Recognition''
-#Electrostastics, VDW interactions, hydrophobic effect, molecular recognition (binding energy)
+:1. Electrostatics, VDW interactions, hydrophobic effect, molecular recognition (binding energy)
-#Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive
+:2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive
-||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.09.11.ams535.rizzo.lect.004.pdf Rizzo, R.]
+||
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.09.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]
 || <center>presentation</center>
 || <center>-</center>
 |-
-| <center>2019.09.14 Mon</center>
+| <center>2020.09.14 Mon</center>
 ||
 *''Intro. to Methods in 3-D Structure Determination''
-#Crystallography, NMR
+:1. Crystallography, NMR
-#Structure Quality, PDB in detail
+:2. Structure Quality, PDB in detail
-||[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.09.16.ams535.rizzo.lect.005.pdf Rizzo, R.]
+||
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.14.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]
 || <center>presentation</center>
 || <center>-</center>
 |-
-| <center>2019.09.16 Wed </center>
+|- style="background:lightgreen"
+| <center>-</center>
+||<center>-</center>
+||<center>-</center>
+||<center>'''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)'''</center>
+||<center>-</center>
+|-
+| <center>2020.09.16 Wed </center>
 ||
-<center>'''Quiz Prior Section I'''</center>
 '''SECTION II: MOLECULAR MODELING'''
 *''Classical Force Fields''
-. All-atom Molecular Mechanics
+:1. All-atom Molecular Mechanics
-. OPLS
+:2. OPLS
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.09.18.AMS535.talk01.pdf Arachchi, Kalani ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.16.AMS535.talk01.mp4 Adams, Dexter 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/2020.09.16.AMS535.talk02.mp4 Chang, Jamie 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/2019.09.23.AMS535.talk01.pdf Chakraborti, Shreyoshi ]
 ||
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Mackerell001.pdf Mackerell, A. D., Jr., Empirical force fields for biological macromolecules: overview and issues. ''J. Comput. Chem.'' '''2004''', ''25'', 1584-604]
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen002.pdf Jorgensen, W. L.; et al., Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. ''J. Am. Chem. Soc.'' '''1996''', ''118'', 11225-11236]
 ||
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/vangunsteren003.pdf van Gunsteren, W. F.; et al., Biomolecular modeling: Goals, problems, perspectives. ''Angew. Chem. Int. Ed. Engl.'' '''2006''', ''45'', 4064-92]
@@ Line 125: / Line 237: @@
 |-
-| <center>2019.09.21 Mon</center>
+| <center>2020.09.21 Mon</center>
 ||
+*''Classical Force Fields''
-#AMBER
+:1. AMBER
 *''Explicit Solvent Models''
-#Water models (TIP3P, TIP4P, SPC)
+:2. Water models (TIP3P, TIP4P, SPC)
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.09.23.AMS535.talk02.pdf He, Miaomiao ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.21.AMS535.talk01.mp4 Corbo, Chris mp4]
+<br>
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.09.25.AMS535.talk01.pdf  Tan, Rodger ]
+[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/2020.09.21.AMS535.talk02.mp4 Chung, So Young mp4]
+<br>
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.21.AMS535.talk02.pdf  pdf]
 ||
@@ Line 142: / Line 257: @@
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen003.pdf Jorgensen, W. L.; et al., Comparison of Simple Potential Functions for Simulating Liquid Water. ''J. Chem. Phys.'' '''1983''', ''79'', 926-935]
 ||
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman005.pdf Bayly, C. I.; et al., A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints For Deriving Atomic Charges - the RESP Model. ''J. Phys. Chem.'' '''1993''', ''97'', 10269-10280]
 |-
+| <center>2020.09.23 Wed </center>
-| <center>2019.09.23 Wed </center>
 ||
+*''Explicit Solvent Models''
-#Condensed-phase calculations (DGhydration)
+:1. Condensed-phase calculations (DGhydration)
+*''Continuum Solvent Models''
+:2. Generalized Born Surface Area (GBSA)
 ||
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.23.AMS535.talk01.mp4  Dovedytis, Matt 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/2019.09.25.AMS535.talk02.pdf  Zhang, Hong ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.23.AMS535.talk02.mp4  Foran, Chris 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/References/Jorgensen010.pdf Jorgensen, W. L.;  et al., Monte Carlo Simulation of Differences in Free Energies of Hydration. ''J. Chem. Phys.'' '''1985''', ''83'', 3050-3054]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen010.pdf Jorgensen, W. L.;  et al., Monte Carlo Simulation of Differences in Free Energies of Hydration. ''J. Chem. Phys.'' '''1985''', ''83'', 3050-3054]
+. [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]
+||
-||<center>-</center>
+<center>-</center>
 |-
-| <center>2019.09.28 Mon</center>
+| <center>2020.09.28 Mon</center>
 ||
 *''Continuum Solvent Models''
-#Generalized Born Surface Area (GBSA)
+:1. Poisson-Boltzmann Surface Area (PBSA)
-#Poisson-Boltzmann Surface Area (PBSA)
+:2. Accuracy of partial atomic changes for GBSA and PBSA
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.09.30.AMS535.talk01.pdf  Zhu, Chuanzhou ]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.09.30.AMS535.talk02.pdf  King, Morgan ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.28.AMS535.talk01.mp4  Hall, Carole 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/2020.09.28.AMS535.talk02_2.mp4  Lang, Liam 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/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/Honig001.pdf Sitkoff, D.; et al., Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. ''J. Phys. Chem.'' '''1994''', ''98'', 1978-1988]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Honig001.pdf Sitkoff, D.; et al., Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. ''J. Phys. Chem.'' 1994, ''98'', 1978-1988]
+.  [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo011.pdf Rizzo, R. C.; et al., Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. ''J. Chem. Theory. Comput.'' '''2006''', ''2'', 128-139]
+||
+<center>-</center>
+|-
-||
+|- style="background:lightgreen"
-. and 2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo011.pdf Rizzo, R. C.; et al., Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. ''J. Chem. Theory. Comput.'' '''2006''', ''2'', 128-139]
+| <center>-</center>
+||<center>-</center>
+||<center>-</center>
+||<center>'''Take home QUIZ for Section 2 starts after today's class (4:00PM) and must be emailed to all Instructors within 24 hours (4:00PM tomorrow)'''</center>
+||<center>'''Additional resources:'''</center>
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Duarte01.pdf Duarte Ramos Matos, G.; et al., Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database. ''J. Chem. Eng. Data'' '''2017''', ''62'', 1559-1569] <br>
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Loeffler01.pdf Loeffler, H. H.; et al., Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages ''J. Chem. Theory Comput.'' '''2018''', ''14'', 5567−5582]
 |-
-| <center>2019.09.30 Wed </center>
+| <center>2020.09.30 Wed </center>
 ||
-<center>'''Quiz Prior Section II'''</center>
 '''SECTION III: SAMPLING METHODS'''
-*''Molecular Conformation''
+*''Molecular Conformations''
-#Small molecules, peptides, relative energy, minimization methods
+:1. Small molecules, peptides, relative energy, minimization methods
+*''Sampling Methods for Large Simulations''
+:2. Molecular dynamics (MD)
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.10.02.AMS535.talk01.pdf  Zhang, Yunlei ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.09.30.AMS535.talk01.mp4  Mingione, Victoria 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/2020.09.30.AMS535.talk02.mp4 Palmeri, Chris 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/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]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Petsko001.pdf Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. ''Nature'' '''1990''', ''347'', 631-9]
 ||
@@ Line 210: / Line 348: @@
 |-
-| <center>2019.10.05 Mon </center>
+| <center>2020.10.05 Mon </center>
 ||
-*''Primary Sampling Methods for Computer Simulations''
+*''Sampling Methods for Large Simulations''
-#Molecular dynamics (MD)
+:1. Monte Carlo (MC)
-#Monte Carlo (MC)
+*''Predicting Protein Structure''
+:2. Ab initio structure prediction (protein-folding)
+||
-||
+. [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/2019.10.07.AMS535.talk01.pdf Wang, Hehe ]
+<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/2019.10.07.AMS535.talk02.pdf Laverty, Scott ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.05.AMS535.talk02.mp4 Quispe-Carbajal, Mariella 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/References/Petsko001.pdf Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. ''Nature'' '''1990''', ''347'', 631-9]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Luke001.pdf Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B.]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Luke001.pdf Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B.]
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen007.pdf Jorgensen, W. L.; TiradoRives, J., Monte Carlo vs Molecular Dynamics for Conformational Sampling. ''J. Phys. Chem.'' '''1996''', ''100'',14508-14513]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill001.pdf Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. ''Nat. Struct. Biol.'' '''1997''', ''4'', 10-19]
 ||
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Metropolis001.pdf Metropolis, N.;et al., Equation of State Calculations by Fast Computing Machines. ''The Journal of Chemical Physics'' '''1953''', ''21'', 1087-1092]
 |-
-| <center>2019.10.07 Wed </center>
+| <center>2020.10.07 Wed </center>
 ||
-*''Predicting Protein Structure I.''
+*''Predicting Protein Structure''
-#Ab initio prediction (protein-folding)
+:1. Example Trp-cage
-#Example Trp-cage
+:2. Comparative (homology) modeling
+||
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.07.AMS535.talk01.mov  Rajesh, Chandana 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/2020.10.07.AMS535.talk02.mp4  Rangwala, Aziz 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/2019.10.09.AMS535.talk01.pdf  Earlie, Ethan ]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.10.09.AMS535.talk02.pdf  Faizi, Aymon ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Simmerling002.pdf Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. ''J. Am. Chem. Soc.'' '''2002''', ''124'',11258-9]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali001.pdf Marti-Renom, M. A.; et al., Comparative protein structure modeling of genes and genomes. ''Annu. Rev. Biophys. Biomol. Struct.'' '''2000''',''29'',291-325]
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill001.pdf Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. ''Nat. Struct. Biol.'' '''1997''', ''4'', 10-19]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Simmerling002.pdf Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. ''J. Am. Chem. Soc.'' '''2002''', ''124'',11258-9]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Fersht001.pdf Daggett, V.; Fersht, A., The present view of the mechanism of protein folding. ''Nat. Rev. Mol. Cell Biol.'' '''2003''', ''4'', 497-502]
-||
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali002.pdf Fiser, A.; et al., Evolution and physics in comparative protein structure modeling. ''Acc. Chem. Res.'' '''2002''', ''35'', 413-21]
--2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Fersht001.pdf Daggett, V.; Fersht, A., The present view of the mechanism of protein folding. ''Nat. Rev. Mol. Cell Biol.'' '''2003''', ''4'', 497-502]
 |-
-| <center>2019.10.12 Mon</center>
+| <center>2020.10.12 Mon</center>
 ||
-*''Predicting Protein Structure II.''
+*''Predicting Protein Structure''
-#Comparative (homology) modeling
+:1. Case studies (CASP)
-#Case studies (CASP)
+:2. Accelerated MD for Blind Protein Prediction
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.10.16.AMS535.talk01.pdf Moalemi, Debbi ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.12.AMS535.talk01.mp4 Sadatrezaei, Golbahar 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/2019.10.16.AMS535.talk02.pdf Pipitone, Karli ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.12.AMS535.talk02.mp4 Steier, Joshua 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/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]
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult002.pdf Moult, J., A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. ''Curr. Opin. Struct. Biol.'' '''2005''',''15'', 285-9]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill002.pdf Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. ''Sci. Adv.'' '''2016''', ''2'']
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali002.pdf Fiser, A.; et al., Evolution and physics in comparative protein structure modeling. ''Acc. Chem. Res.'' '''2002''', ''35'', 413-21]
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Moult003.pdf Kryshtafovych, A.; et al., Progress over the first decade of CASP experiments. ''Proteins'' '''2005''', ''61 Suppl 7'', 225-36]
 |-
+| <center>2020.10.14 Wed</center>
+||
+*''Predicting Protein Structure''
+:1. MD x-ray refinement
+:2. Protein Design
+||
-| <center>2019.10.14 Wed</center>
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.14.AMS535.talk01.mp4 Contorno, Shaymus mp4]
-||
+<br>
-*''Predicting Protein Structure Part III''
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.14.AMS535.talk01.pdf  pdf]
-#Accelerated MD for Blind Protein Prediction
-#MD x-ray refinement
-||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.10.21.AMS535.talk01.pdf Stepanenko, Darya  ]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.10.21.AMS535.talk02.pdf Ertem, Fatma ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.14.AMS535.talk02.mp4 He, Yongle 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/References/Dill002.pdf Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. ''Sci. Adv.'' '''2016''', ''2'']
+. [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/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/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/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]
+|-
+|- style="background:lightgreen"
+| <center>-</center>
+||<center>-</center>
+||<center>-</center>
+||<center>'''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)'''</center>
+||<center>-</center>
 |-
+| <center>2020.10.19 Mon </center>
-| <center>2019.10.19 Mon </center>
 ||
-<center>'''Quiz Prior Section III'''</center>
 '''SECTION IV: LEAD DISCOVERY'''
-*''Docking I.''
+*''Docking''
-#Introduction to DOCK
+:1. Introduction to DOCK
+:2. Test Sets (pose reproduction)
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.10.23.AMS535.talk01.pdf Telehany, Stephen ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.19.AMS535.talk01.mp4 Hetherington, Caitlin 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/2020.10.19.AMS535.talk02.mp4 Koller, Angus 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/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/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/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>2019.10.21 Wed</center>
+| <center>2020.10.21 Wed</center>
 ||
-*''Docking II.''
+*''Docking''
-#Test Sets (binding modes)
+:1. Test Sets (virtual screening)
-#Test Sets (virtual screening)
+:2. Test Sets (database enrichment)
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.10.28.AMS535.talk01.pdf Samoilova, Khristina ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.21.AMS535.talk01.mp4 Pak, Steven 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/2019.10.28.AMS535.talk02.pdf He, Miaomiao ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.21.AMS535.talk02.mp4 Adams, Dexter 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/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/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://www.ccdc.cam.ac.uk/products/life_sciences/gold/validation/astex/ The CCDC/Astex Test Set]
 . [http://zinc.docking.org ZINC Website at UCSF, Shoichet group]
 |-
-| <center>2019.10.26 Mon</center>
+| <center>2020.10.26 Mon</center>
 ||
-*''Docking III.''
+*''Docking''
-#''Database Enrichment''
+:1. Footprint-based scoring
-#''Footprint-based scoring''
+*''Discovery Methods''
+:2. Hotspot probes (GRID)
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.10.30.AMS535.talk01.pdf Chakraborti, Shreyoshi ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.26.AMS535.talk01.mp4 Chang, Jaime 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/2019.10.30.AMS535.talk02.pdf Zhang, Hong  ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.26.AMS535.talk02.mp4 Corbo, Chris 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/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.]
-. [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/Goodford001.pdf Goodford, P. J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. ''J. Med. Chem.'' '''1985''', ''28'', 849-57]
 ||
 <center>-</center>
 |-
-| <center>2019.10.28 Wed</center>
+| <center>2020.10.28 Wed</center>
 ||
-*''Discovery Methods I.''
+*''Discovery Methods''
-#Hotspot probes (GRID)
+:1. COMFA
-#COMFA
+:2 Pharmacophores
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.11.04.AMS535.talk01.pdf Zhu, Chuanzhou ]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.11.04.AMS535.talk02.pdf Arachchi, Kalani ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.10.28.AMS535.talk01.mp4 Chung, So Young 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/2020.10.28.AMS535.talk02.mp4 Dovedytis, Matt 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/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/Kubinyi002.pdf Kubinyi, H., Comparative molecular field analysis (CoMFA). ''Encyclopedia of Computational Chemistry, Databases and Expert Systems Section'', John Wiley & Sons, Ltd. '''1998''']
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Swaan001.pdf Chang, C.; et al., Pharmacophore-based discovery of ligands for drug transporters. ''Advanced Drug Delivery Reviews'' '''2006''', ''58'', 1431-1450]
 ||
@@ Line 382: / Line 562: @@
 |-
-| <center>2019.11.02 Mon</center>
+| <center>2020.11.02 Mon</center>
 ||
-*''Discovery Methods II.''
+*''Discovery Methods.''
-#Pharmacophores in drug design #1
+:1. Pharmacophores
-#Pharmacophores in drug design #2
+:2. De novo design
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.11.06.AMS535.talk01.pdf  McHugh, Ryan  ]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.11.06.AMS535.talk02.pdf  King, Morgan ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.02.AMS535.talk01.mp4 Foran, Chris 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/2020.11.02.AMS535.talk02.mp4 Hall, Carole 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/References/Swaan001.pdf Chang, C.; et al., Pharmacophore-based discovery of ligands for drug transporters. ''Advanced Drug Delivery Reviews'' '''2006''', ''58'', 1431-1450]
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Alvarez001.pdf Alvarez, J.; et al., Pharmacophore-Based Molecular Docking to Account for Ligand Flexibility. ''Proteins'' '''2003''', ''51'', 172-188 ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shakhnovich001.pdf Cheron, N.; et al., OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188]
 ||<center>-</center>
 |-
-| <center>2019.11.04 Wed</center>
+| <center>2020.11.04 Wed</center>
 ||
-*''Discovery Methods III.''
+*''Discovery Methods''
-#De novo design
+:1. De novo design
-#Genetic Algorithm
+:2. Genetic Algorithm
 ||
-. & 2.  ''Presentation''
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.04.AMS535.talk01.mp4 Lang, Liam 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/2019.11.11.AMS535.talk01.pdf  Prentis, Lauren ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.04.AMS535.talk02.mp4 Mingione, Victoria 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/References/Jorgensen016.pdf Jorgensen, W.; et al., Efficient drug lead discovery and optimization. ''Acc. of Chem. Research'' '''2009''', ''42 (6)'', 724-733]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shakhnovich001.pdf Cheron, N.; et al., OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188]
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pegg001.pdf Pegg, S. C.; Haresco, J. J.; Kuntz, I. D., A genetic algorithm for structure-based de novo design. ''J Comput Aided Mol Des'' '''2001''', ''15'', 911-33]
+||<center>-</center>
+|-
+|- style="background:lightgreen"
+| <center>-</center>
+||<center>-</center>
+||<center>-</center>
+||<center>'''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)'''</center>
 ||<center>-</center>
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen016.pdf Jorgensen, W.; et al., Efficient drug lead discovery and optimization. ''Acc. of Chem. Research'' '''2009''', ''42 (6)'', 724-733]
 |-
-| <center>2019.11.09 Mon</center>
+| <center>2020.11.09 Mon</center>
 ||
-<center>'''Quiz Prior Section IV'''</center>
 '''SECTION V: LEAD REFINEMENT
-*''Free Energy Perturbation (FEP)''
+*''Free Energy Methods''
-#Thermolysin with two ligands
+:1. Thermolysin with two ligands (FEP)
+:2. Fatty acid synthase I ligands (TI)
+||
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.09.AMS535.talk01.mp4  Palmeri, Chris 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/2020.11.09.AMS535.talk02.mp4  Pasumarthy, Sishir mp4]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.11.13.AMS535.talk01.pdf  Wang, Hehe]
+<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/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]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/labahn001.pdf Labahn, A.; et al., Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I. ''Bioorg Med Chem.'' '''2012''', ''20'', 3446-53]
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen006.pdf Jorgensen, W. L., Free Energy Calculations:  A Breakthrough for Modeling Organic Chemistry in Solution. ''Accounts Chem. Res.'' '''1989''', ''22'', 184-189]
+&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen006.pdf Jorgensen, W. L., Free Energy Calculations:  A Breakthrough for Modeling Organic Chemistry in Solution. ''Accounts Chem. Res.'' '''1989''', ''22'', 184-189]
+&2. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman007.pdf Kollman, P., Free Energy Calculations:  Applications to Chemical and Biochemical Phenomena. ''Chem. Rev.'' '''1993''', ''93'', 2395-2417]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman007.pdf Kollman, P., Free Energy Calculations:  Applications to Chemical and Biochemical Phenomena. ''Chem. Rev.'' '''1993''', ''93'', 2395-2417]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lawrenz001.pdf Lawrenz, M.; et al., Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. ''J. Chem. Theory Comput.'' '''2009''', ''5'', 1106-1116]
 |-
-| <center>2019.11.11 Wed</center>
+| <center>2020.11.11 Wed</center>
 ||
-*''Thermodynamic integration''
 *'' MM-PB/GBSA''
-#Free energy calculation using TI
+:1. Intro to Molecular Mechanics Poisson-Boltzmann / Generalized Born Surface Area Methods
-#Intro to Molecular Mechanics Poisson-Boltzmann / Generalized Born Surface Area Methods
+*''MM-GBSA case studies''
+:2. EGFR and mutants
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.11.18.AMS535.talk01.pdf  Zhang, Yunlei  ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.11.AMS535.talk01.mp4  Quispe-Carbajal, Mariella  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/2019.11.18.AMS535.talk02.pdf  Moalemi, Debbi ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.11.AMS535.talk02.mp4  Rajesh, Chandana  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/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]
 . [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman012.pdf Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. ''Accounts Chem. Res.'' '''2000''', ''33'', 889-897]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo019.pdf Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. ''Biochemistry'', '''2009''', ''48'', 8435-8448]
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lawrenz001.pdf Lawrenz, M.; et al., Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. ''J. Chem. Theory Comput.'' '''2009''', ''5'', 1106-1116]
 |-
-| <center>2019.11.16 Mon </center>
+| <center>2020.11.16 Mon </center>
 ||
 *''MM-GBSA case studies''
-#EGFR and mutants
+:1. ErbB family selectivity
-#ErbB family selectivity
+*''Linear Response''
+:2. Intro to Linear Response (LR method)
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.11.20.AMS535.talk01.pdf Faizi, Aymon ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.16.AMS535.talk01.mp4 Rangwala, Aziz 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/2019.11.20.AMS535.talk02.pdf Earlie, Ethan ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.16.AMS535.talk02.mp4 Sadatrezaei, Golbahar 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/References/rizzo019.pdf Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. ''Biochemistry'', '''2009''', ''48'', 8435-8448]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo024.pdf Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, ''Biochemistry'', '''2012''', ''51'', 2390-2406]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo024.pdf Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, ''Biochemistry'', '''2012''', ''51'', 2390-2406]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Aqvist001.pdf Aqvist, J.; Mowbray, S. L., Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations. ''J Biol Chem'' '''1995''', ''270'', 9978-81]
 ||<center>-</center>
 |-
-| <center>2019.11.18 Wed </center>
+| <center>2020.11.18 Wed </center>
 ||
 *''Linear Response''
-#Intro to Linear Response (LR method)
+:1. Inhibition of protein kinases (Extended LR method)
-#Inhibition of protein kinases (Extended LR method)
+*''Properties of Known Drugs''
+:2. Molecular Scaffolds (frameworks) and functionality (side-chains
+||
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.18.AMS535.talk01.mp4  Steier, Joshua 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/2020.11.18.AMS535.talk02.mp4  Contorno, Shaymus 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/2019.11.25.AMS535.talk01.pdf  Stepanenko, Darya ]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.11.25.AMS535.talk02.pdf  Fatma, Ertem ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen001.pdf Tominaga, Y.; Jorgensen, W. L.; General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. ''J. Med. Chem.'' '''2004''', ''47'', 2534-2549]
-||
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko001.pdf Bemis, G. W.; Murcko, M. A., The properties of known drugs. 1. Molecular frameworks. ''J. Med. Chem.'' '''1996''', ''39'', 2887-93]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Aqvist001.pdf Aqvist, J.; Mowbray, S. L., Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations. ''J Biol Chem'' '''1995''', ''270'', 9978-81]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen001.pdf Tominaga, Y.; Jorgensen, W. L.; General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. ''J. Med. Chem.'' '''2004''', ''47'', 2534-2549]
+. [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>
@@ Line 500: / Line 723: @@
 |- style="background:peachpuff"
-| <center>2019.11.23 Mon</center>
+| <center>2020.11.23 Mon</center>
 ||
 *''No Class: Thanksgiving''
 ||<center>-</center>
 ||<center>-</center>
 ||<center>-</center>
 |-
 |- style="background:peachpuff"
-| <center>2019.11.23 Wed</center>
+| <center>2020.11.25 Wed</center>
 ||
 *''No Class: Thanksgiving''
 ||<center>-</center>
 ||<center>-</center>
 ||<center>-</center>
 |-
+| <center>2020.11.30 Mon </center>
+||
+*''Properties of Known Drugs''
+:1. Lipinski Rule of Five
+:2 ADME Prediction
+||
-| <center>2019.11.30 Mon </center>
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.AMS535.talk01.mp4  He, Yongle 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/2020.11.30.AMS535.talk02.mp4   Hetherington, Caitlin mp4]
+<br>
+[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.AMS535.talk02.pdf  pdf]
 ||
-*''Properties of Known Drugs''
-#Molecular Scaffolds (frameworks) and functionality (side-chains)
-#Lipinski Rule of Five
-||
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski002.pdf Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. ''Adv. Drug. Deliv. Rev.'' '''2001''', ''46'', 3-26]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.12.02.AMS535.talk01.pdf  Basu, Rajeswari ]
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.12.02.AMS535.talk02.pdf  Samoilova, Khristina ]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu001.pdf Hou, T. J.; Xu, X. J.; ADME evaluation in drug discovery. ''J. Mol. Model'', '''2002''', ''8'', 337-349]
 ||
-. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko001.pdf Bemis, G. W.; Murcko, M. A., The properties of known drugs. 1. Molecular frameworks. ''J. Med. Chem.'' '''1996''', ''39'', 2887-93]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski001.pdf Lipinski, C. A., Chris Lipinski discusses life and chemistry after the Rule of Five. ''Drug. Discov. Today'' '''2003''', ''8'', 12-6]
-. [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]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu003.pdf Hou, T. J.; Xu, X. J.; AMDE Evaluation in drug discovery 3. Modeling blood-brain barrier partitioning using simple molecular descriptors. ''J. Chem. Inf. Comput. Sci.'', '''2003''', ''43'', 2137-2152]
+|-
+|-
+| <center>2020.12.02 Wed </center>
+||
+*''Properties of Known Drugs''
+:1. Synthetic Accessibility
+:2. QED
+||
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.12.02.AMS535.talk01.mp4  Koller, Angus 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/References/Lipinski002.pdf Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. ''Adv. Drug. Deliv. Rev.'' '''2001''', ''46'', 3-26]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.12.02.AMS535.talk02.mp4   Pak, Steve 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/References/Lipinski001.pdf Lipinski, C. A., Chris Lipinski discusses life and chemistry after the Rule of Five. ''Drug. Discov. Today'' '''2003''', ''8'', 12-6]
+. [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]
+. [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bickerton2012.pdf Bickerton, G. R., Quantifying the chemical beauty of drugs. ''Nature Chemistry'' '''2012''', ''4'', 90-98]
+||<center>-</center>
 |-
-| <center>2019.12.02 Wed </center>
+| <center>2020.12.07 Mon </center>
 ||
-*'' Review for Final Exam''
+*Course Wrap up
+||<center>[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020.11.30.ams535_thermo_cycles_study_guide.pdf Thermodynamic Cycles]
+[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>
 ||<center>-</center>
-|| [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.12.04.ams535_final_study_guide.pdf final_exam_study_guide]
 ||<center>-</center>
 |-
-| <center>2019.12.07 Mon </center>
+|- style="background:lightgreen"
-||
+| <center>-</center>
-*'' Review for Last Quiz''
+||<center>-</center>
 ||<center>-</center>
-||
+||<center>'''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)'''</center>
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2019.12.04.ams535_final_study_guide.pdf final_exam_study_guide]
-[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/thermo_cycles.pdf Thermodynamic Cycles]
 ||<center>-</center>
 |-
@@ Line 574: / Line 812: @@
 |-
 |}
+== '''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 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.