Difference between revisions of "2024 AMS-535 Fall"

Latest revision as of 10:50, 6 November 2024

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

Instructors	Dr. Robert C. Rizzo [631-632-8519, rizzorc -at- gmail.com] Brock Boysan [631-632-8519, brock dot boysan -at- stonybrook dot edu]
Course No.	AMS-535 / CHE-535
Location/Time	FREY HALL 326 WESTCAMPUS, MoWe 2:00PM - 3:20PM
Office Hours	Anytime by appointment, Math Tower 3-129
Grading	Grades will be based on the quality of: (1) Oral presentations (25%) Student will give 1-2 oral presentations (in-person) based on papers assigned from the schedule below. (2) Class discussion (25%) Before each class, course participants will read the papers that are to be orally presented and come prepared to ask thoughtful questions and participate in scientific discussion about the topics being presented. (3) Quizzes (50%) Five in class quizzes will be assigned based on the 5 major sections of the course and the lowest quiz grade will be dropped.

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

Learning Objectives

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

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

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

Syllabus Notes

General Information:

This is an in-person course. There is no online section.
Note that course grading criteria has been modified from previous years (see grading breakdown above).
The first 5 lectures are to help put everyone on an even footing with regards to background material and will be given by the Instructors at the regularly scheduled class time.
All class correspondence should be addressed to ALL course Instructors.

Oral Presentations:

Each participant will give 1-2 oral presentations (depending on the class size).
In-person presentations should be formal (as if at a scientific meeting or job talk), presented in PPT format, and be 20-25 minutes long.
All presentations will be posted on the course website.
References should occur at the bottom of each slide when necessary.
Presentations should be based mostly on the primary references however secondary references and other sources may be required to make some presentations complete.
It is the responsibility of each presenter to email a PPT file of their talk by Friday at 5PM before the week in which their talk is being discussed.
In general, talks will likely be arranged in the following order: (1) Introduction/Background (include biological relevance if applicable), (2) Specifics of the System or General Problem, (3) Computational Methods (theory) and Details (system setup) being used, (4) Results and Discussion (critical interpretation of results and any problems/challenges), (5) Conclusions/Future, and (6) Acknowledgments.
Everyone in the class will evaluate each of the oral presentations using a Presentation Assessment Sheet

Class Discussion:

A sizable portion of the course grade is based on participating in Class Discussion. Thus, it is important that everyone attend all of the classes and participate in scientific discussion to receive full credit.
If a student is unable to attend a specific class for reasons beyond their control they will instead be asked to email the instructor(s) AND submit a one page Paper Summary Sheet answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Class Discussion" part of their grade for any classes that were missed.
If a student misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted.

Quizzes:

Five quizzes will be used to assess student understanding of the course material.
The quiz format is in-class, closed book, estimate at 30 minutes per quiz.
Answers to quiz questions should integrate topics, concepts, and outcomes of the different papers covered for the section being tested.
Students are expected to work alone and do their own work. Representing another person's work as your own is always wrong. The Instructors are required to report any and all suspected instances of academic dishonesty to the students Graduate Program Director.
If a student misses a quiz because of illness they must provide written documentation (Doctors Note) in order to take a makeup quiz.

Class Schedule

Date	Topic	Speaker and Presentation	Primary Reference	Secondary Reference
2024.08.26 Mon	First Day Class Organizational Meeting	Rizzo, R	Course introduction and format. Go over Syllabus. Course participant background and introductions.	-
-	-	-	START SECTION I: DRUG DISCOVERY AND BIOMOLECULAR STRUCTURE	-
2024.08.28 Wed	Drug Discovery 1. Introduction, history, irrational vs. rational 2. Viral Target Examples	Rizzo, R. lecture slides 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	Rizzo, R. prior recorded lecture 1 mp4
2024.09.02 Mon	-	-	NO CLASS - LABOR DAY	-
2024.09.04 Wed	Chemistry Review 1. Molecular structure, bonding, graphical representations 2. Functionality, properties of organic molecules	Rizzo, R. lecture slides pdf	in class lecture	Rizzo, R. prior recorded lecture 2 mp4
2024.09.09 Mon	Biomolecular Structure 1. Lipids, carbohydrates 2. Nucleic acids, proteins	Rizzo, R. lecture slides pdf	in class lecture	Rizzo, R. prior recorded lecture 3 mp4 Structures/definitions of the 20 amino acid side chains used for this class pdf
2024.09.11 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. lecture slides pdf	in class lecture	Rizzo, R. prior recorded lecture 4 mp4
2024.09.16 Mon	Intro. to Methods in 3-D Structure Determination 1. Crystallography, NMR 2. Structure Quality, PDB in detail	Rizzo, R. lecture slides pdf	in class lecture	Rizzo, R. prior recorded lecture 5 mp4
-	-	-	START SECTION II: MOLECULAR MODELING after QUIZ #1	-
2024.09.18 Wed	Classical Force Fields 1. All-atom Molecular Mechanics	QUIZ #1 1. Gauer, Aiden pdf	1. Mackerell, A. D., Jr., Empirical force fields for biological macromolecules: overview and issues. J. Comput. Chem. 2004, 25, 1584-604	1. van Gunsteren, W. F.; et al., Biomolecular modeling: Goals, problems, perspectives. Angew. Chem. Int. Ed. Engl. 2006, 45, 4064-92
2024.09.23 Mon	Classical Force Fields 1. OPLS 2. AMBER	1. Saha, Satyaki pdf 2. Fatema, Kaniz pdf	1. Jorgensen, W. L.; et al., Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. J. Am. Chem. Soc. 1996, 118, 11225-11236 2. 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	1. Jorgensen, W. L.; et al., The Opls Potential Functions For Proteins - Energy Minimizations For Crystals of Cyclic-Peptides and Crambin. J. Am. Chem. Soc. 1988, 110, 1657-1671 2. 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
2024.09.25 Wed	Explicit Solvent Models 1. Water models (TIP3P, TIP4P, SPC) 2. Condensed-phase calculations (DGhydration)	1. James, Breanna pdf 2. Akinboade, Modinat pdf	1. Jorgensen, W. L.; et al., Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 1983, 79, 926-935 2. Jorgensen, W. L.; et al., Monte Carlo Simulation of Differences in Free Energies of Hydration. J. Chem. Phys. 1985, 83, 3050-3054	2. Thermodynamic Cycle as Drawn By Dr. Rizzo
2024.09.30 Mon	Continuum Solvent Models 1. Generalized Born Surface Area (GBSA) 2. Poisson-Boltzmann Surface Area (PBSA)	1. Gebauer, Emma pdf 2. pdf	1. Still, W. C.; et al., Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. J. Am. Chem. Soc 1990, 112, 6127-6129 2. Sitkoff, D.; et al., Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. J. Phys. Chem. 1994, 98, 1978-1988	-
-	-	-	'START SECTION III: SAMPLING METHODS after QUIZ #2	-
2024.10.02 Wed	Molecular Conformations 1. Small molecules, peptides, relative energy, minimization methods	QUIZ #2 1. Averkava, Veranika 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	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
2024.10.07 Mon	Sampling Methods for Large Simulations 1. Molecular dynamics (MD) 2. Monte Carlo (MC)	1. Lu, Hongbo pdf 2. Kalinowski, Nicole pdf	1. Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. Nature 1990, 347, 631-9 2. Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B.	2. Jorgensen, W. L.; TiradoRives, J., Monte Carlo vs Molecular Dynamics for Conformational Sampling. J. Phys. Chem. 1996, 100,14508-14513 2. Metropolis, N.;et al., Equation of State Calculations by Fast Computing Machines. The Journal of Chemical Physics 1953, 21, 1087-1092
2024.10.09 Wed	Predicting Protein Structure 1. Ab initio structure prediction (protein-folding) 2. Example Trp-cage	1. Kennedy, Christopher pdf 2. Jordan, Claire pdf	1. Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. Nat. Struct. Biol. 1997, 4, 10-19 2. Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. J. Am. Chem. Soc. 2002, 124,11258-9	2. 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
2024.10.14 Mon	-	-	NO CLASS - FALL BREAK	-
2024.10.16 Wed	Predicting Protein Structure 1. Comparative (homology) modeling 2. Accelerated MD for Blind Protein Prediction	1. Behboodian, Ali pdf 2. Parwana, Diksha pdf	1. Marti-Renom, M. A.; et al., Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 2000,29,291-325 2. Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. Sci. Adv. 2016, 2	-
2024.10.21 Mon	Predicting Protein Structure 1. Alpha Fold 2. Meso-Scale MD (Markov State Models)	1. Bickel, John pdf 2. Bickel, John pdf	1. Senior, A.;et al, Improved protein structure prediction using potentials from deep learning. Nature 2020, 577, 1-5 2. Durrant, J.;et al, Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ACS Central Science 2020, 6, 189-196	2. Husic, B.; et al., Markov State Models: From an Art to a Science. JACS 2018, 140, 2386-2396
-	-	-	START SECTION IV: LEAD DISCOVERY after QUIZ #3	-
2024.10.23 Wed	SECTION IV: LEAD DISCOVERY Docking 1. Introduction to DOCK	QUIZ #3 1. O'Reilly, Owen pdf	1. Allen, W. J.; et al., DOCK 6: Impact of New Features and Current Docking Performance. Journal of computational chemistry 2015, 36, 1132-1156.	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
2024.10.28 Mon	Docking 1. Test Sets (database enrichment) 2. Test Sets (virtual screening)	1. Corbo, Chris pdf 2.Corbo, Chris pdf]	1. Mysinger, M.; et al., Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. Journal of medicinal chemistry 2012, 55, 6582-94 2. 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. ZINC Website at UCSF, Shoichet group
2024.10.30 Wed	Docking 1. Footprint-based scoring Discovery Methods 2. Hotspot probes (GRID)	1. Boysan, Brock pdf 2. Boysan, Brock 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	-
2024.11.04 Mon	Discovery Methods 1. COMFA 2. Pharmacophores	1. Okisamen, Benjamin pdf 2. Rufrano, Michael 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
2024.11.06 Wed	Discovery Methods. 1. Pharmacophores 2. De novo design	1. No oral presentation however paper will be on the next quiz. 2. Spector, Evan 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	-
2024.11.11 Mon	Discovery Methods 1. De novo design 2. Genetic Algorithm	1. Pak, Steven pdf 2. Ogunfolakan, Oyindamola pdf	1. Jorgensen, W.; et al., Efficient drug lead discovery and optimization. Acc. of Chem. Research 2009, 42 (6), 724-733 2. Prentis, L and Singleton, C et al.; A molecular evolution algorithm for ligand design in DOCK J Comp Chem 2022, 43 (29), 1942-1963	-
-	-	-	START SECTION V: LEAD REFINEMENT after QUIZ #4	-
2024.11.13 Wed	Free Energy Methods 1. Thermolysin with two ligands (FEP)	QUIZ #4 1. Wray, Zahra 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	1. Bartlett, P. A.; Marlowe, C. K., Evaluation of Intrinsic Binding Energy from a Hydrogen Bonding Group in an Enzyme Inhibitor. Science. 1987, 235, 569-571 1. Tronrud, D.E.; Holden, H.M.; Matthews, B.W.; Structures of Two Thermolysin-Inhibitor Complexes That Differ by a Single Hydrogen Bond. Science 1987, 235, 571-573 1. Jorgensen, W. L., Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution. Accounts Chem. Res. 1989, 22, 184-189 1. Kollman, P., Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. Chem. Rev. 1993, 93, 2395-2417
2024.11.18 Mon	Thermodynamic Integration 1. Fatty acid synthase I ligands MM-PB/GBSA 2. Intro to Molecular Mechanics Poisson-Boltzmann / Generalized Born Surface Area Methods	1. Seecharan, Vanie pdf 2. Hailegeorgis, Derara pdf	1. Labahn, A.; et al., Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I. Bioorg Med Chem. 2012, 20, 3446-53 2. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts Chem. Res. 2000, 33, 889-897	1. 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
2024.11.20 Wed	MM-GBSA case studies" 1. EGFR and mutants 2. ErbB family selectivity	1. Rizzo, Rob pdf 2. Rizzo, Rob pdf	1. Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. Biochemistry, 2009, 48, 8435-8448 2. Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, Biochemistry, 2012, 51, 2390-2406	-
2024.11.25 Mon	Linear Response 1. Intro to Linear Response (LR method) 2. Inhibition of protein kinases (Extended LR method)	1. Kwan, Isabelle pdf 2. Reisel, Alexander pdf	1. Aqvist, J.; Mowbray, S. L., Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations. J Biol Chem 1995, 270, 9978-81 2. 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	-
2024.11.27 Wed	-	-	NO CLASS: THANKSGIVING	-
2024.12.02 Mon	Properties of Known Drugs 1. Molecular Scaffolds (frameworks) and functionality (side-chains) 2. Lipinski Rule of Five	1. Boysan, Brock pdf 2. Boysan, Brock pdf	1. Bemis, G. W.; Murcko, M. A., The properties of known drugs. 1. Molecular frameworks. J. Med. Chem. 1996, 39, 2887-93 1. Bemis, G. W.; Murcko, M. A., Properties of known drugs. 2. Side chains. J. Med. Chem. 1999, 42, 5095-9 2. 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. Lipinski, C. A., Chris Lipinski discusses life and chemistry after the Rule of Five. Drug. Discov. Today 2003, 8, 12-6
2024.12.04 Wed	Properties of Known Drugs 1. Drug likeness 2. Descriptor-driven design	1. Pak, Steven pdf 2. Pak, Steven pdf	1. Bickerton, G. R., Quantifying the chemical beauty of drugs. Nature Chemistry 2012, 4, 90-98 2. Matos, DRG; Pak, S; Rizzo R; Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit. J. Chem. Inf. Model. 2023
-	-	-	Class Wrap up after QUIZ #5	-
2024.12.09 Mon	Last Day Class	QUIZ #5	-	-

Required Syllabi Statements:

The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php

Student Accessibility Support Center Statement: If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities and search Fire Safety and Evacuation and Disabilities.

Academic Integrity Statement: Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html

Critical Incident Management: Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php

Difference between revisions of "2024 AMS-535 Fall"

Latest revision as of 10:50, 6 November 2024

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

Syllabus Notes

Class Schedule

Required Syllabi Statements:

Navigation menu

Personal tools

Namespaces

Variants

Views

More

Search

Navigation

Rizzo Lab

Courses

Toolbox

@@ Line 8: / Line 8: @@
 | Dr. Robert C. Rizzo    [631-632-8519, rizzorc -at- gmail.com]
-Steven Pak  [631-632-8519, steven dot pak -at- stonybrook dot edu]
+Brock Boysan [631-632-8519, brock dot boysan -at- stonybrook dot edu]
-John Bickel [631-632-8519, john dot bickel -at- stonybrook dot edu]
 |-
 | '''Course No.''' || AMS-535  / CHE-535
 |-
-| '''Location/Time''' || Mathematics S235S, Monday and Wednesday 2:30PM - 3:50PM
+| '''Location/Time''' || FREY HALL 326 WESTCAMPUS, MoWe 2:00PM - 3:20PM
 |-
 | '''Office Hours''' || Anytime by appointment, Math Tower 3-129
@@ Line 20: / Line 19: @@
 | '''Grading''' ||  Grades will be based on the quality of: <br>
-(1) Pre-recorded oral presentations (25%)
+(1) Oral presentations (25%)
-::Student will pre-record 1-2 ZOOM presentations based on papers assigned from the schedule below which will be uploaded to the class wiki for viewing by class participants <br>
+::Student will give 1-2 oral presentations (in-person) based on papers assigned from the schedule below. <br>
-(2) Class discussion (30%)
+(2) Class discussion (25%)
-::At scheduled class times, students will attend class in-person and discuss the papers they have read and the presentations they have watched.  For each paper, each student will prepare 2 thoughtful questions ahead of time to facilitate scientific discussion. Copies of these questions will be handed to the instructors prior to the beginning of discussion.
+::Before each class, course participants will read the papers that are to be orally presented and come prepared to ask thoughtful questions and participate in scientific discussion about the topics being presented.<br>
-(3) In-class quizzes (45%)
+(3) Quizzes (50%)
-::Five in class quizzes will be assigned based on the 5 major sections of the course and the lowest quiz grade will be dropped.
+::Five in class quizzes will be assigned based on the 5 major sections of the course and the lowest quiz grade will be dropped.<br>
 |-
 |}
 <br>
 '''GENERAL INFORMATION:''' AMS-535 provides an introduction to the field of computational structure-based drug design. The course aims to foster collaborative learning and will consist of presentations by instructors, course participants, and guest lecturers arranged in five major sections outlined below. Presentations should aim to summarize key papers, theory, and application of computational methods relevant to computational drug design. Grade will be based on oral presentations, class discussion/attendance/participation, and quizzes.
@@ Line 50: / Line 50: @@
 == '''Syllabus Notes''' ==
-This is a mixed course meaning that there will be both synchronous and asynchronous aspects. Note that course grading criteria has been modified from previous years (see grading breakdown above). Other details for this semester are as follows:
 '''General Information:'''
-*We will hold class at the regularly scheduled time (M/W 2:30-3:50PM) and class will be held in person.  There is no online section.
+*This is an in-person course. There is no online section.
+*Note that course grading criteria has been modified from previous years (see grading breakdown above).
 *The first 5 lectures are to help put everyone on an even footing with regards to background material and will be given by the Instructors at the regularly scheduled class time.
 *All class correspondence should be addressed to ALL course Instructors.
-'''Discussion Sessions:'''
+'''Oral Presentations:'''
-*The bulk of the classes will be devoted to in-person discussion, in breakout groups, facilitated by an assigned discussion leader. Papers will be read prior to meeting (1-2 per class) for which everyone will also have watched an oral presentation on the paper (1-2 per class). Oral presentations will be in the form of pre-recorded videos made by students taking the class.
+*Each participant will give 1-2 oral presentations (depending on the class size).
-*For each paper discussed, one (1) student in each discussion group will be assigned as discussion leader. The discussion group leader <b> will be expected </b> to understand and guide discussion on the paper. If there is any confusion regarding paper content as a discussion leader, students should reach out to TAs well before the class in which they are to lead.
+*In-person presentations should be formal (as if at a scientific meeting or job talk), presented in PPT format, and be 20-25 minutes long.
-*The Instructors(s) will moderate and participate in discussion, as well as field questions and clear up any misunderstandings, and take over discussion when necessary.
+*All presentations will be posted on the course website.
-*For each paper, each student will prepare 2 thoughtful questions ahead of time to facilitate scientific discussion. Copies of these questions will be handed to the instructors prior to the beginning of discussion.
+*References should occur at the bottom of each slide when necessary.
-*A sizeable portion of the class grade (30%) is based on these discussion sections. Thus, it is important that everyone attend all of the classes <b> and participate in each discussion </b> to receive full credit.
+*Presentations should be based mostly on the primary references however secondary references and other sources may be required to make some presentations complete.
-*If a student is unable to attend a specific class for reasons beyond their control they will instead be asked to email the instructor(s) AND submit a one page  [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.paper.summary.docx Paper Summary Sheet] answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Discussion" part of their grade for any synchronous classes that were missed.
+*It is the responsibility of each presenter to email a PPT file of their talk by Friday at 5PM before the week in which their talk is being discussed.
+*In general, talks will likely be arranged in the following order: (1) Introduction/Background (include biological relevance if applicable), (2) Specifics of the System or General Problem, (3) Computational Methods (theory) and Details (system setup) being used, (4) Results and Discussion (critical interpretation of results and any problems/challenges), (5) Conclusions/Future, and (6) Acknowledgments.
+*Everyone in the class will evaluate each of the oral presentations using a [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.presentation.assessment.docx Presentation Assessment Sheet]
+'''Class Discussion:'''
+*A sizable portion of the course grade is based on participating in Class Discussion. Thus, it is important that everyone attend all of the classes <b> and participate in scientific discussion </b> to receive full credit.
+*If a student is unable to attend a specific class for reasons beyond their control they will instead be asked to email the instructor(s) AND submit a one page  [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.paper.summary.docx Paper Summary Sheet] answering questions about the papers that were discussed on the day that they missed. The "Paper Summary Sheets" will form the basis of the "Class Discussion" part of their grade for any classes that were missed.
 *If a student misses a class they will have 24 hours to submit their Paper Summary Sheets. Late Paper Summary Sheets will not be accepted.
-'''Oral Presentations:'''
+'''Quizzes:'''
-*Students will pre-record 1-2 ZOOM presentations based on papers assigned to them from the schedule shown below.
-*Students will email their pre-recorded presentations to ALL course Instructors by Friday at 5PM before the week in which their presentations will be discussed.
-*Course participants will watch the student presentations and, independently, read the paper before the class in which they are to be discussed.
-*Course participants will score each student presentation using a [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2020_ams.che535.presentation.assessment.docx Presentation Assessment Sheet] which will be emailed to ALL Instructors within 24 hours after the class in which the presentation was discussed.
-'''In-class Quizzes:'''
 *Five quizzes will be used to assess student understanding of the course material.
-*The quiz format is in-class, closed book.
+*The quiz format is in-class, closed book, estimate at 30 minutes per quiz.
 *Answers to quiz questions should integrate topics, concepts, and outcomes of the different papers covered for the section being tested.
-*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 are expected to work alone and do their own work. Representing another person's work as your own is always wrong. The Instructors are required to report any and all suspected instances of academic dishonesty to the students Graduate Program Director.
+*If a student misses a quiz because of illness they must provide written documentation (Doctors Note) in order to take a makeup quiz.
-'''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>
@@ Line 105: / Line 84: @@
 {| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"
 |- style="background:cornflowerblue"
-|| <center>'''Date'''</center>
+| style="width: 5%" | <center>'''Date'''</center>
-|| <center>'''Topic'''</center>
+| style="width: 20%" | <center>'''Topic'''</center>
-|| <center>'''Speaker and Presentation'''</center>
+| style="width: 15%" | <center>'''Speaker and Presentation'''</center>
-|| <center>'''Primary Reference'''</center>
+| style="width:30%" | <center>'''Primary Reference'''</center>
-|| <center>'''Secondary Reference'''</center>
+| style="width: 30%" | <center>'''Secondary Reference'''</center>
 |-
-| <center>2023.08.28 Mon</center>
+| <center>2024.08.26 Mon</center>
 ||
+*''First Day Class''
 *''Organizational Meeting''
 || Rizzo, R
@@ Line 128: / Line 108: @@
 |-
-| <center>2023.08.30 Wed</center>
+| <center>2024.08.28 Wed</center>
 ||
 *''Drug Discovery''
@@ Line 134: / Line 114: @@
 :2. Viral Target Examples
 ||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.08.30.ams535.rizzo.lect.001.pdf Rizzo, R. pdf]
+Rizzo, R. <br>
+lecture slides [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.08.28.ams535.rizzo.lect.001.pdf pdf]
 ||
 :1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen009.pdf Jorgensen, W.L., The many roles of computation in drug discovery. ''Science'' '''2004''', ''303'', 1813-8]
 :2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz004.pdf Kuntz, I. D., Structure-based strategies for drug design and discovery. ''Science'' '''1992''', ''257'', 1078-1082]
 ||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.mp4 Rizzo, R. prior recorded lecture 1 mp4]
+Rizzo, R. <br>
+prior recorded lecture 1 [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.24.ams535.rizzo.lect.001.mp4 mp4]
 |-
 |- style="background:peachpuff"
-|| <center>2023.09.04 Mon</center>
+|| <center>2024.09.02 Mon</center>
 ||<center>-</center>
 ||<center>-</center>
@@ Line 150: / Line 132: @@
 |-
-| <center>2023.09.06 Wed</center>
+| <center>2024.09.04 Wed</center>
 ||
 *''Chemistry Review''
@@ Line 156: / Line 138: @@
 :2. Functionality, properties of organic molecules
 ||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.pdf Rizzo, R. pdf]
+Rizzo, R. <br>
+lecture slides [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.04.ams535.rizzo.lect.002.pdf pdf]
 ||
 <center>in class lecture</center>
 ||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.mp4 Rizzo, R. prior recorded lecture 2 mp4]
+Rizzo, R. <br>
+prior recorded lecture 2 [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.29.ams535.rizzo.lect.002.mp4 mp4]
 |-
-| <center>2023.09.11 Mon</center>
+| <center>2024.09.09 Mon</center>
 ||
 *''Biomolecular Structure''
@@ Line 169: / Line 153: @@
 :2. Nucleic acids, proteins
 ||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.pdf Rizzo, R. pdf]
+Rizzo, R. <br>
+lecture slides [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.09.ams535.rizzo.lect.003.pdf pdf]
 ||
 <center>in class lecture</center>
 ||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.mp4 Rizzo, R. prior recorded lecture 3 mp4]
+Rizzo, R. <br>
-<br>
+prior recorded lecture 3 [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.08.31.ams535.rizzo.lect.003.mp4 mp4]
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/2010.amino_acids_scanned.pdf structures of the 20 amino acid side chains]
+<br><br>
+Structures/definitions of the 20 amino acid side chains used for this class [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/2010.amino_acids_scanned.pdf pdf]
 |-
+| <center>2024.09.11 Wed</center>
-| <center>2023.09.13 Wed</center>
 ||
 *''Molecular Interactions and Recognition''
@@ Line 185: / Line 170: @@
 :2. Inhibitors types: allosteric, transition state, covalent vs non-covalent, selective, competitive
 ||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.pdf Rizzo, R. pdf]
+Rizzo, R. <br>
+lecture slides [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.11.ams535.rizzo.lect.004.pdf pdf]
 ||
 <center>in class lecture</center>
 ||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.mp4 Rizzo, R. prior recorded lecture 4 mp4]
+Rizzo, R. <br>
+prior recorded lecture 4 [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.07.ams535.rizzo.lect.004.mp4 mp4]
 |-
-| <center>2023.09.18 Mon</center>
+| <center>2024.09.16 Mon</center>
 ||
 *''Intro. to Methods in 3-D Structure Determination''
@@ Line 198: / Line 185: @@
 :2. Structure Quality, PDB in detail
 ||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022.09.12.ams535.rizzo.lect.005.pdf Rizzo, R. pdf]
+Rizzo, R. <br>
+lecture slides [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.16.ams535.rizzo.lect.005.pdf pdf]
 ||
 <center>in class lecture</center>
 ||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.13.ams535.rizzo.lect.005.mp4 Rizzo, R. prior recorded lecture 5 mp4]
+Rizzo, R. <br>
+prior recorded lecture 5 [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021.09.13.ams535.rizzo.lect.005.mp4 mp4]
 |-
@@ Line 212: / Line 201: @@
 ||<center>-</center>
 |-
-| <center>2023.09.20 Wed</center>
+| <center>2024.09.18 Wed </center>
 ||
 * ''Classical Force Fields''
-:1. Quiz #1
+:1. All-atom Molecular Mechanics
-:2. All-atom Molecular Mechanics
+||
-||
+'''QUIZ #1''' <br> <br>
-:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.09.20.AMS535.talk01.mp4 Alseika, Zachary mp4]
+. Gauer, Aiden <br>
-:[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.09.20.AMS535.talk01.pdf  pdf]
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.18.AMS535.talk01.pdf pdf]
+<br> <br>
 ||
-:2 [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Mackerell001.pdf Mackerell, A. D., Jr., Empirical force fields for biological macromolecules: overview and issues. ''J. Comput. Chem.'' '''2004''', ''25'', 1584-604]
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Mackerell001.pdf Mackerell, A. D., Jr., Empirical force fields for biological macromolecules: overview and issues. ''J. Comput. Chem.'' '''2004''', ''25'', 1584-604]
 ||
-:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/vangunsteren003.pdf van Gunsteren, W. F.; et al., Biomolecular modeling: Goals, problems, perspectives. ''Angew. Chem. Int. Ed. Engl.'' '''2006''', ''45'', 4064-92]
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/vangunsteren003.pdf van Gunsteren, W. F.; et al., Biomolecular modeling: Goals, problems, perspectives. ''Angew. Chem. Int. Ed. Engl.'' '''2006''', ''45'', 4064-92]
 |-
+| <center>2024.09.23 Mon</center>
-| <center>2023.09.25 Mon</center>
 ||
 * ''Classical Force Fields''
@@ Line 233: / Line 222: @@
 :2. AMBER
 ||
-:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.09.25.AMS535.talk01.mp4 Pina, Liliana mp4] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.09.25.AMS535.talk01.pdf  pdf]
+. Saha, Satyaki <br>
-:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.09.25.AMS535.talk02.mp4 Bickel, John mp4] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.09.25.AMS535.talk02.pdf  pdf]
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.23.AMS535.talk01.pdf pdf]
+<br> <br>
+. Fatema, Kaniz <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.23.AMS535.talk02.pdf pdf]
 ||
 :1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen002.pdf Jorgensen, W. L.; et al., Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. ''J. Am. Chem. Soc.'' '''1996''', ''118'', 11225-11236]
@@ Line 243: / Line 235: @@
 |-
-| <center>2023.09.27 Wed </center>
+| <center>2024.09.25 Wed </center>
 ||
 *''Explicit Solvent Models''
@@ Line 249: / Line 241: @@
 :2. Condensed-phase calculations (DGhydration)
 ||
-:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.09.27.AMS535.talk01.mp4  Boysan, Brock mp4] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.09.27.AMS535.talk01.pdf   pdf]
+. James, Breanna <br>
-:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.09.27.AMS535.talk02.mp4 Dwulit, Catherine mp4] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.09.27.AMS535.talk02.pdf   pdf]
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.25.AMS535.talk01.pdf pdf]
+<br> <br>
+. Akinboade, Modinat <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.25.AMS535.talk02.pdf pdf]
 ||
 :1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen003.pdf Jorgensen, W. L.; et al., Comparison of Simple Potential Functions for Simulating Liquid Water. ''J. Chem. Phys.'' '''1983''', ''79'', 926-935]
@@ Line 256: / Line 251: @@
 ||
 :2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/DDGhyd_cycle.pdf Thermodynamic Cycle as Drawn By Dr. Rizzo]
+|-
-|-
+| <center>2024.09.30 Mon</center>
-| <center>2023.10.02 Mon</center>
 ||
 *''Continuum Solvent Models''
 :1. Generalized Born Surface Area (GBSA)
 :2. Poisson-Boltzmann Surface Area (PBSA)
 ||
-:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.02.AMS535.talk01.mp4  Bushati, Aldo mp4] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.02.AMS535.talk01.pdf  pdf]
+. Gebauer, Emma <br>
-:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.02.AMS535.talk02.mp4  Dreher, Kathleen mp4] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.02.AMS535.talk02.pdf  pdf]
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.30.AMS535.talk01.pdf pdf]
+<br> <br>
+.  <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.09.30.AMS535.talk02.pdf pdf]
 ||
 :1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Still001.pdf Still, W. C.; et al., Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. ''J. Am. Chem. Soc'' 1990, ''112'', 6127-6129]
@@ Line 278: / Line 275: @@
 ||<center>-</center>
 ||<center>-</center>
-||<center>'''IN CLASS QUIZ for Section 2 2023.10.04 WED'''</center>
+||<center>''''START SECTION III: SAMPLING METHODS <br> after <br> QUIZ #2'''</center>
-||<center>'''Additional resources:'''</center>
+||<center>-</center>
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Duarte01.pdf Duarte Ramos Matos, G.; et al., Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database. ''J. Chem. Eng. Data'' '''2017''', ''62'', 1559-1569] <br>
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Loeffler01.pdf Loeffler, H. H.; et al., Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages ''J. Chem. Theory Comput.'' '''2018''', ''14'', 5567−5582]
 |-
-| <center>2023.10.04 Wed </center>
+| <center>2024.10.02 Wed </center>
 ||
-'''SECTION III: SAMPLING METHODS'''
 *''Molecular Conformations''
 :1. Small molecules, peptides, relative energy, minimization methods
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.04.AMS535.talk01.mp4  Kim, Joseph mp4]
+||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.04.AMS535.talk01.pdf   pdf]
+'''QUIZ #2''' <br> <br>
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman011.pdf Howard, A. E.; Kollman, P. A., An analysis of current methodologies for conformational searching of complex molecules. ''J. Med. Chem.'' '''1988''', ''31'', 1669-75]
+. Averkava, Veranika <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.02.AMS535.talk01.pdf pdf]
+<br> <br>
+||
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman011.pdf Howard, A. E.; Kollman, P. A., An analysis of current methodologies for conformational searching of complex molecules. ''J. Med. Chem.'' '''1988''', ''31'', 1669-75]
+||
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Colby_College_MMtutor.pdf Section 4 (PAGES 22-27) Colby College Molecular Mechanics Tutorial Introduction, 2004, Shattuck, T.W., Colby College]
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Holloway001.pdf Holloway, M. K., A priori prediction of ligand affinity by energy minimization. ''Perspect. Drug Discov. Design'' '''1998''', ''9-11'', 63-84]
+|-
+| <center>2024.10.07 Mon </center>
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Colby_College_MMtutor.pdf Section 4 (PAGES 22-27) Colby College Molecular Mechanics Tutorial Introduction, 2004, Shattuck, T.W., Colby College]
+||
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Holloway001.pdf Holloway, M. K., A priori prediction of ligand affinity by energy minimization. ''Perspect. Drug Discov. Design'' '''1998''', ''9-11'', 63-84]
-|- style="background:peachpuff"
-  | <center>2023.10.09 Mon</center>
-  |
-*''No Class: Fall Break''
-  | <center>-</center>
-  | <center>-</center>
-  | <center>-</center>
-|-
-  | <center>2023.10.11 Wed </center>
-  |
 *''Sampling Methods for Large Simulations''
 :1. Molecular dynamics (MD)
 :2. Monte Carlo (MC)
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.11.AMS535.talk01.mp4 Zhu, Zeru mp4]
+||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.11.AMS535.talk01.pdf  pdf]
+. Lu, Hongbo <br>[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.07.AMS535.talk01.pdf pdf]
+<br> <br>
+. Kalinowski, Nicole <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.07.AMS535.talk02.pdf pdf]
+||
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Petsko001.pdf Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. ''Nature'' '''1990''', ''347'', 631-9]
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Luke001.pdf Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B.]
+||
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen007.pdf Jorgensen, W. L.; TiradoRives, J., Monte Carlo vs Molecular Dynamics for Conformational Sampling. ''J. Phys. Chem.'' '''1996''', ''100'',14508-14513]
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Metropolis001.pdf Metropolis, N.;et al., Equation of State Calculations by Fast Computing Machines. ''The Journal of Chemical Physics'' '''1953''', ''21'', 1087-1092]
+|-
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.11.AMS535.talk02.mp4 Wodzenski, Nicholas mp4] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.11.AMS535.talk02.pdf  pdf]
+| <center>2024.10.09 Wed </center>
+||
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Petsko001.pdf Karplus, M.; Petsko, G. A., Molecular dynamics simulations in biology. ''Nature'' '''1990''', ''347'', 631-9]
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Luke001.pdf Metropolis Monte Carlo Simulation Tutorial, LearningFromTheWeb.net, Accessed Oct 2008, Luke, B.]
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen007.pdf Jorgensen, W. L.; TiradoRives, J., Monte Carlo vs Molecular Dynamics for Conformational Sampling. ''J. Phys. Chem.'' '''1996''', ''100'',14508-14513]
-  | 2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Metropolis001.pdf Metropolis, N.;et al., Equation of State Calculations by Fast Computing Machines. ''The Journal of Chemical Physics'' '''1953''', ''21'', 1087-1092]
-|-
-  | <center>2023.10.16 Mon </center>
-  |
 *''Predicting Protein Structure''
 :1. Ab initio structure prediction (protein-folding)
-*''Predicting Protein Structure''
 :2. Example Trp-cage
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.16.AMS535.talk01.mp4  Corbo, Chris mp4] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.16.AMS535.talk01.pdf   pdf]
+||
+. Kennedy, Christopher <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.09.AMS535.talk01.pdf pdf]
+<br> <br>
+. Jordan, Claire <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.09.AMS535.talk02.pdf pdf]
+||
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill001.pdf Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. ''Nat. Struct. Biol.'' '''1997''', ''4'', 10-19]
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Simmerling002.pdf Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. ''J. Am. Chem. Soc.'' '''2002''', ''124'',11258-9]
+||
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Fersht001.pdf Daggett, V.; Fersht, A., The present view of the mechanism of protein folding. ''Nat. Rev. Mol. Cell Biol.'' '''2003''', ''4'', 497-502]
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali002.pdf Fiser, A.; et al., Evolution and physics in comparative protein structure modeling. ''Acc. Chem. Res.'' '''2002''', ''35'', 413-21]
+|-
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.16.AMS535.talk02.mp4  Dharan, Aishwarya mp4] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.16.AMS535.talk02.pdf   pdf]
+|- style="background:peachpuff"
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill001.pdf Dill, K. A.; Chan, H. S., From Levinthal to pathways to funnels. ''Nat. Struct. Biol.'' '''1997''', ''4'', 10-19]
+|| <center>2024.10.14 Mon</center>
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Simmerling002.pdf Simmerling, C.;et al., All-atom structure prediction and folding simulations of a stable protein. ''J. Am. Chem. Soc.'' '''2002''', ''124'',11258-9]
+|| <center>-</center>
-  | 2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Fersht001.pdf Daggett, V.; Fersht, A., The present view of the mechanism of protein folding. ''Nat. Rev. Mol. Cell Biol.'' '''2003''', ''4'', 497-502]
+|| <center>-</center>
+||<center>'''NO CLASS - FALL BREAK'''</center>
+|| <center>-</center>
+|-
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali002.pdf Fiser, A.; et al., Evolution and physics in comparative protein structure modeling. ''Acc. Chem. Res.'' '''2002''', ''35'', 413-21]
+| <center>2024.10.16 Wed</center>
-|-
+||
-  | <center>2023.10.18 Wed</center>
-  |
 *''Predicting Protein Structure''
 :1. Comparative (homology) modeling
-:2. Neural Network
+:2. Accelerated MD for Blind Protein Prediction
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.18.AMS535.talk01.mp4 Kang, Sung Jin mp4][https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.18.AMS535.talk01.pdf  pdf]
+||
+. Behboodian, Ali <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.16.AMS535.talk01.pdf pdf]
+<br> <br>
+. Parwana, Diksha <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.16.AMS535.talk02.pdf pdf]
+||
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali001.pdf Marti-Renom, M. A.; et al., Comparative protein structure modeling of genes and genomes. ''Annu. Rev. Biophys. Biomol. Struct.'' '''2000''',''29'',291-325]
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill002.pdf Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. ''Sci. Adv.'' '''2016''', ''2'']
+|| <center>-</center>
+|-
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.18.AMS535.talk02.mp4 Glukhov, Ernest mp4] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.18.AMS535.talk02.pdf  pdf]
+| <center>2024.10.21 Mon</center>
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Sali001.pdf Marti-Renom, M. A.; et al., Comparative protein structure modeling of genes and genomes. ''Annu. Rev. Biophys. Biomol. Struct.'' '''2000''',''29'',291-325]
+||
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Hassabis001.pdf Senior, A.;et al, Improved protein structure prediction using potentials from deep learning. ''Nature'' '''2020''', ''577'', 1-5]
-  |
-|-
-  | <center>2023.10.23 Mon</center>
-  |
 *''Predicting Protein Structure''
-:1. Accelerated MD for Blind Protein Prediction
+:1. Alpha Fold
 :2. Meso-Scale MD (Markov State Models)
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.23.AMS535.talk01.mp4 Aywa, Khalayi mp4 ] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.23.AMS535.talk01.pdf  pdf]
+||
+. Bickel, John <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.21.AMS535.talk01.pdf pdf]
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.23.AMS535.talk02.mp4 Bickel, John mp4 ] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.23.AMS535.talk02.pdf   pdf ]
+<br> <br>
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Dill002.pdf Perez, A.; et al., Blind protein structure prediction using accelerated free-energy simulations. ''Sci. Adv.'' '''2016''', ''2'']
+. Bickel, John <br>
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Amaro001.pdf Durrant, J.;et al, Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ''ACS Central Science'' '''2020''', ''6'', 189-196]
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.21.AMS535.talk02.pdf pdf]
-  | 2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pande002.pdf Husic, B.; et al., Markov State Models: From an Art to a Science. ''JACS'' '''2018''', ''140'', 2386-2396]
+||
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Hassabis001.pdf Senior, A.;et al, Improved protein structure prediction using potentials from deep learning. ''Nature'' '''2020''', ''577'', 1-5]
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Amaro001.pdf Durrant, J.;et al, Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism. ''ACS Central Science'' '''2020''', ''6'', 189-196]
+||
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Pande002.pdf Husic, B.; et al., Markov State Models: From an Art to a Science. ''JACS'' '''2018''', ''140'', 2386-2396]
 |-
@@ Line 367: / Line 379: @@
 ||<center>-</center>
 ||<center>-</center>
-||<center>'''IN CLASS QUIZ for Section 3 2023.10.25 WED'''</center>
+||<center>'''START SECTION IV: LEAD DISCOVERY <br> after <br>  QUIZ #3'''</center>
 ||<center>-</center>
 |-
-| <center>2023.10.25 Wed </center>
+| <center>2024.10.23 Wed </center>
 ||
 '''SECTION IV: LEAD DISCOVERY'''
 *''Docking''
 :1. Introduction to DOCK
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.25.AMS535.talk01.mp4 Corbo, Chris mp4] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.25.AMS535.talk01.pdf   pdf]
+||
+'''QUIZ #3''' <br> <br>
+. O'Reilly, Owen <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.23.AMS535.talk01.pdf pdf]
+<br> <br>
+||
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo035.pdf Allen, W. J.; et al., DOCK 6: Impact of New Features and Current Docking Performance. ''Journal of computational chemistry'' '''2015''', ''36'', 1132-1156.]
+||
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz002.pdf Ewing, T. J.; et al., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. ''J. Comput. Aided Mol. Des.'' '''2001''', ''15'', 411-28]
+|-
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo035.pdf Allen, W. J.; et al., DOCK 6: Impact of New Features and Current Docking Performance. ''Journal of computational chemistry'' '''2015''', ''36'', 1132-1156.]
+| <center>2024.10.28 Mon</center>
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kuntz002.pdf Ewing, T. J.; et al., DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. ''J. Comput. Aided Mol. Des.'' '''2001''', ''15'', 411-28]
+||
-|-
+*''Docking''
-  | <center>2023.10.30 Mon</center>
-  | *''Docking''
 :1. Test Sets (database enrichment)
 :2. Test Sets (virtual screening)
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.30.AMS535.talk01.mp4 Dreher, Kathleen mp4] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.30.AMS535.talk01.pdf   pdf]
+||
+. Corbo, Chris <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.28.AMS535.talk01.pdf pdf]
+<br> <br>
+.Corbo, Chris <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.28.AMS535.talk02.pdf pdf]]
+||
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet003.pdf Mysinger, M.; et al., Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. ''Journal of medicinal chemistry'' '''2012''', ''55'', 6582-94]
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet001.pdf Irwin, J. J.; Shoichet, B. K., ZINC--a free database of commercially available compounds for virtual screening. ''J. Chem. Inf. Model.'' '''2005''', ''45'', 177-82]
+||
+:2. [https://zinc.docking.org ZINC Website at UCSF, Shoichet group]
+|-
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.30.AMS535.talk02.mp4 Bushati, Aldo mp4] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.10.30.AMS535.talk02.pdf   pdf]]
+| <center>2024.10.30 Wed</center>
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet003.pdf Mysinger, M.; et al., Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. ''Journal of medicinal chemistry'' '''2012''', ''55'', 6582-94]
+||
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shoichet001.pdf Irwin, J. J.; Shoichet, B. K., ZINC--a free database of commercially available compounds for virtual screening. ''J. Chem. Inf. Model.'' '''2005''', ''45'', 177-82]
-  | 2. [https://zinc.docking.org ZINC Website at UCSF, Shoichet group]
-|-
-  | <center>2023.11.01 Wed</center>
-  |
 *''Docking''
 :1. Footprint-based scoring
@@ Line 400: / Line 424: @@
 *''Discovery Methods''
 :2. Hotspot probes (GRID)
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.01.AMS535.talk01.mp4 Nguyen, An Phuc mp4]
+||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.01.AMS535.talk01.pdf   pdf]
+. Boysan, Brock <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.30.AMS535.talk01.pdf pdf]
+<br> <br>
+. Boysan, Brock <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.10.30.AMS535.talk02.pdf pdf]
+||
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo022.pdf Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. ''J. Comput. Chem.'' '''2011''', ''32'', 2273-2289.]
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Goodford001.pdf Goodford, P. J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. ''J. Med. Chem.'' '''1985''', ''28'', 849-57]
+||<center>-</center>
+|-
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.01.AMS535.talk02.mp4 Boysan, Brock mp4]
+| <center>2024.11.04 Mon</center>
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.01.AMS535.talk02.pdf  pdf]
+||
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo022.pdf Balius, T.E.; et al., Implementation and Evaluation of a Docking-Rescoring Method Using Molecular Footprint Comparisons. ''J. Comput. Chem.'' '''2011''', ''32'', 2273-2289.]
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Goodford001.pdf Goodford, P. J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. ''J. Med. Chem.'' '''1985''', ''28'', 849-57]
-  |
-|-
-  | <center>2023.11.06 Mon</center>
-  |
 *''Discovery Methods''
 :1. COMFA
-:2 Pharmacophores
+:2. Pharmacophores
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.06.AMS535.talk01.mp4 Alseika, Zachary mp4] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.06.AMS535.talk01.pdf  pdf]
+||
+. Okisamen, Benjamin <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.04.AMS535.talk01.pdf pdf]
+<br> <br>
+. Rufrano, Michael <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.04.AMS535.talk02.pdf pdf]
+||
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kubinyi002.pdf Kubinyi, H., Comparative molecular field analysis (CoMFA). ''Encyclopedia of Computational Chemistry, Databases and Expert Systems Section'', John Wiley & Sons, Ltd. '''1998''']
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Swaan001.pdf Chang, C.; et al., Pharmacophore-based discovery of ligands for drug transporters. ''Advanced Drug Delivery Reviews'' '''2006''', ''58'', 1431-1450]
+||
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bunce001.pdf Cramer, R. D.; Patterson, D. E.; Bunce, J. D., Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. ''J. Am. Chem. Soc.'', ''1988'', ''110'', 5959-5967]
+|-
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.06.AMS535.talk02.mp4 Dwulit, Catherine mp4] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.06.AMS535.talk02.pdf  pdf]
+| <center>2024.11.06 Wed</center>
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kubinyi002.pdf Kubinyi, H., Comparative molecular field analysis (CoMFA). ''Encyclopedia of Computational Chemistry, Databases and Expert Systems Section'', John Wiley & Sons, Ltd. '''1998''']
+||
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Swaan001.pdf Chang, C.; et al., Pharmacophore-based discovery of ligands for drug transporters. ''Advanced Drug Delivery Reviews'' '''2006''', ''58'', 1431-1450]
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bunce001.pdf Cramer, R. D.; Patterson, D. E.; Bunce, J. D., Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. ''J. Am. Chem. Soc.'', ''1988'', ''110'', 5959-5967]
-|-
-  | <center>2023.11.08 Wed</center>
-  |
 *''Discovery Methods.''
 :1. Pharmacophores
 :2. De novo design
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.08.AMS535.talk01.mp4 Zhu, Zeru mp4]
+||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.08.AMS535.talk01.pdf  pdf]
+. No oral presentation however paper will be on the next quiz. <br>
+<br> <br>
+. Spector, Evan <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.06.AMS535.talk02.pdf pdf]
+||
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Alvarez001.pdf Alvarez, J.; et al., Pharmacophore-Based Molecular Docking to Account for Ligand Flexibility. ''Proteins'' '''2003''', ''51'', 172-188 ]
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shakhnovich001.pdf Cheron, N.; et al., OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188]
+||<center>-</center>
+|-
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.08.AMS535.talk02.mp4 Corbo, Chris mp4]
+| <center>2024.11.11 Mon</center>
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.08.AMS535.talk02.pdf  pdf]
+||
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Alvarez001.pdf Alvarez, J.; et al., Pharmacophore-Based Molecular Docking to Account for Ligand Flexibility. ''Proteins'' '''2003''', ''51'', 172-188 ]
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Shakhnovich001.pdf Cheron, N.; et al., OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. ''J. Med. Chem.'' '''2016''', ''59'', 4171-4188]
-  | <center>-</center>
-|-
-  | <center>2023.11.13 Mon</center>
-  |
 *''Discovery Methods''
 :1. De novo design
 :2. Genetic Algorithm
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.13.AMS535.talk01.mp4 Pak, Steven mp4]
+||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.13.AMS535.talk01.pdf  pdf]
+. Pak, Steven <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.11.AMS535.talk01.pdf pdf]
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.13.AMS535.talk02.mp4 Bickel, John mp4]
+<br> <br>
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.13.AMS535.talk02.pdf  pdf]
+. Ogunfolakan, Oyindamola <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.11.AMS535.talk02.pdf pdf]
+||
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen016.pdf Jorgensen, W.; et al., Efficient drug lead discovery and optimization. ''Acc. of Chem. Research'' '''2009''', ''42 (6)'', 724-733]
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen016.pdf Jorgensen, W.; et al., Efficient drug lead discovery and optimization. ''Acc. of Chem. Research'' '''2009''', ''42 (6)'', 724-733]
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/PrentisSingleton001.pdf Prentis, L and Singleton, C et al.; A molecular evolution algorithm for ligand design in DOCK ''J Comp Chem'' '''2022''', ''43 (29)'', 1942-1963]
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/PrentisSingleton001.pdf Prentis, L and Singleton, C et al.; A molecular evolution algorithm for ligand design in DOCK ''J Comp Chem'' '''2022''', ''43 (29)'', 1942-1963]
 ||<center>-</center>
 |-
@@ Line 460: / Line 491: @@
 ||<center>-</center>
 ||<center>-</center>
-||<center>'''IN CLASS QUIZ for Section 4 2023.11.15 WED'''</center>
+||<center>'''START SECTION V: LEAD REFINEMENT <br> after <br> QUIZ #4'''</center>
 ||<center>-</center>
 |-
-| <center>2023.11.15 Wed</center>
+| <center>2024.11.13 Wed </center>
 ||
-'''SECTION V: LEAD REFINEMENT
 *''Free Energy Methods''
 :1. Thermolysin with two ligands (FEP)
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.15.AMS535.talk01.mp4  Kang, Sung Jin mp4]
+||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.15.AMS535.talk01.pdf   pdf]
+'''QUIZ #4''' <br> <br>
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman009.pdf Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A., Calculation of the relative change in binding free energy of a protein-inhibitor complex. ''Science'' '''1987''', ''235'', 574-6]
+. Wray, Zahra <br>
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/tronrud002.pdf Tronrud, D.E.; Holden, H.M.; Matthews, B.W.; Structures of Two Thermolysin-Inhibitor Complexes That Differ by a Single Hydrogen Bond. ''Science'' '''1987''', ''235'', 571-573]
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.13.AMS535.talk01.pdf pdf]
+<br> <br>
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen006.pdf Jorgensen, W. L., Free Energy Calculations:  A Breakthrough for Modeling Organic Chemistry in Solution. ''Accounts Chem. Res.'' '''1989''', ''22'', 184-189]
+||
+. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman009.pdf Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A., Calculation of the relative change in binding free energy of a protein-inhibitor complex. ''Science'' '''1987''', ''235'', 574-6]
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman007.pdf Kollman, P., Free Energy Calculations:  Applications to Chemical and Biochemical Phenomena. ''Chem. Rev.'' '''1993''', ''93'', 2395-2417]
+||
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/bartlett000.pdf Bartlett, P. A.;  Marlowe, C. K., Evaluation of Intrinsic Binding Energy from a Hydrogen Bonding Group in an Enzyme Inhibitor. ''Science.'' '''1987''', ''235'',  569-571]
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/tronrud002.pdf Tronrud, D.E.; Holden, H.M.; Matthews, B.W.; Structures of Two Thermolysin-Inhibitor Complexes That Differ by a Single Hydrogen Bond. ''Science'' '''1987''', ''235'', 571-573]
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen006.pdf Jorgensen, W. L., Free Energy Calculations:  A Breakthrough for Modeling Organic Chemistry in Solution. ''Accounts Chem. Res.'' '''1989''', ''22'', 184-189]
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman007.pdf Kollman, P., Free Energy Calculations:  Applications to Chemical and Biochemical Phenomena. ''Chem. Rev.'' '''1993''', ''93'', 2395-2417]
 |-
-  | <center>2023.11.20 Mon</center>
-  |
-*''Free Energy Methods''
-:1. Fatty acid synthase I ligands (TI)
+| <center>2024.11.18 Mon</center>
+||
+*''Thermodynamic Integration''
+:1. Fatty acid synthase I ligands
 *'' MM-PB/GBSA''
 :2. Intro to Molecular Mechanics Poisson-Boltzmann / Generalized Born Surface Area Methods
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.20.AMS535.talk01.mp4  Dharan, Aishwarya mp4] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.20.AMS535.talk01.pdf   pdf]
+||
+. Seecharan, Vanie <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.18.AMS535.talk01.pdf pdf]
+<br> <br>
+. Hailegeorgis, Derara <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.18.AMS535.talk02.pdf pdf]
+||
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/labahn001.pdf Labahn, A.; et al., Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I. ''Bioorg Med Chem.'' '''2012''', ''20'', 3446-53]
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman012.pdf Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. ''Accounts Chem. Res.'' '''2000''', ''33'', 889-897]
+||
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lawrenz001.pdf Lawrenz, M.; et al., Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. ''J. Chem. Theory Comput.'' '''2009''', ''5'', 1106-1116]
+|-
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.20.AMS535.talk02.mp4  Pina, Liliana mp4] [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.20.AMS535.talk02.pdf   pdf]
+| <center>2024.11.20 Wed </center>
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/labahn001.pdf Labahn, A.; et al., Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I. ''Bioorg Med Chem.'' '''2012''', ''20'', 3446-53]
+||
+*''MM-GBSA case studies"
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Kollman012.pdf Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. ''Accounts Chem. Res.'' '''2000''', ''33'', 889-897]
+:1. EGFR and mutants
-  | 1. See above papers
+:2. ErbB family selectivity
+||
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lawrenz001.pdf Lawrenz, M.; et al., Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. ''J. Chem. Theory Comput.'' '''2009''', ''5'', 1106-1116]
+. Rizzo, Rob <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.20.AMS535.talk01.pdf pdf]
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/bartlett000.pdf Bartlett, P. A.;  Marlowe, C. K., Evaluation of Intrinsic Binding Energy from a Hydrogen Bonding Group in an Enzyme Inhibitor. ''Science.'' '''1987''', ''235'',  569-571]
+<br> <br>
-|- style="background:peachpuff"
+. Rizzo, Rob <br>
-  | <center>2021.11.22 Wed</center>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.20.AMS535.talk02.pdf pdf]
-  |
+||
-*''No Class: Thanksgiving''
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo019.pdf Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. ''Biochemistry'', '''2009''', ''48'', 8435-8448]
-  | <center>-</center>
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo024.pdf Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, ''Biochemistry'', '''2012''', ''51'', 2390-2406]
-  | <center>-</center>
+||<center>-</center>
-  | <center>-</center>
 |-
-  | <center>2023.11.27 Mon </center>
-  | *''MM-GBSA case
-:1. EGFR and mutantsstudies''
-:2. ErbB family selectivity
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.27.AMS535.talk01.mp4 Rizzo, Robert mp4]
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.27.AMS535.talk01.pdf  pdf]
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.27.AMS535.talk02.mp4 Aywa, Khalayi mp4][https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.27.AMS535.talk02.pdf  pdf]
+| <center>2024.11.25 Mon </center>
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo019.pdf Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. ''Biochemistry'', '''2009''', ''48'', 8435-8448]
+||
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo024.pdf Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, ''Biochemistry'', '''2012''', ''51'', 2390-2406]
-  | <center>-</center>
-|-
-  | <center>2023.11.29 Wed </center>
-  |
 *''Linear Response''
 :1. Intro to Linear Response (LR method)
 :2. Inhibition of protein kinases (Extended LR method)
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.29.AMS535.talk01.mp4  Wodzenski, Nicholas mp4]
+||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.29.AMS535.talk01.pdf  pdf]
+. Kwan, Isabelle <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.25.AMS535.talk01.pdf pdf]
+<br> <br>
+. Reisel, Alexander <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.11.25.AMS535.talk02.pdf pdf]
+||
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Aqvist001.pdf Aqvist, J.; Mowbray, S. L., Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations. ''J Biol Chem'' '''1995''', ''270'', 9978-81]
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen001.pdf Tominaga, Y.; Jorgensen, W. L.; General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. ''J. Med. Chem.'' '''2004''', ''47'', 2534-2549]
+|| <center>-</center>
+|-
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.29.AMS535.talk02.mp4  Glukhov, Ernest mp4]
+|- style="background:peachpuff"
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.11.29.AMS535.talk02.pdf  pdf]
+| <center>2024.11.27 Wed</center>
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Aqvist001.pdf Aqvist, J.; Mowbray, S. L., Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations. ''J Biol Chem'' '''1995''', ''270'', 9978-81]
+|| <center>-</center>
+|| <center>-</center>
+|| <center> '''NO CLASS: THANKSGIVING''' </center>
+|| <center>-</center>
+|-
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Jorgensen001.pdf Tominaga, Y.; Jorgensen, W. L.; General model for estimation of the inhibition of protein kinases using Monte Carlo simulations. ''J. Med. Chem.'' '''2004''', ''47'', 2534-2549]
+| <center>2024.12.02 Mon </center>
-  | <center>-</center>
+||
-|-
-  | <center>2023.12.04 Mon </center>
-  |
 *''Properties of Known Drugs''
 :1. Molecular Scaffolds (frameworks) and functionality (side-chains)
 :2. Lipinski Rule of Five
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.12.04.AMS535.talk01.mp4 Kim, Joseph mp4]
+||
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.12.04.AMS535.talk01.pdf  pdf]
+. Boysan, Brock <br>
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.12.02.AMS535.talk01.pdf pdf]
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.12.04.AMS535.talk02.mp4  Boysan, Brock mp4]
+<br> <br>
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.12.04.AMS535.talk02.pdf  pdf]
+. Boysan, Brock <br>
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko001.pdf Bemis, G. W.; Murcko, M. A., The properties of known drugs. 1. Molecular frameworks. ''J. Med. Chem.'' '''1996''', ''39'', 2887-93]
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.12.02.AMS535.talk02.pdf pdf]
+||
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko002.pdf Bemis, G. W.; Murcko, M. A., Properties of known drugs. 2. Side chains. ''J. Med. Chem.'' '''1999''', ''42'', 5095-9]
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko001.pdf Bemis, G. W.; Murcko, M. A., The properties of known drugs. 1. Molecular frameworks. ''J. Med. Chem.'' '''1996''', ''39'', 2887-93]
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Murcko002.pdf Bemis, G. W.; Murcko, M. A., Properties of known drugs. 2. Side chains. ''J. Med. Chem.'' '''1999''', ''42'', 5095-9]
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski002.pdf Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. ''Adv. Drug. Deliv. Rev.'' '''2001''', ''46'', 3-26]
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski002.pdf Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. ''Adv. Drug. Deliv. Rev.'' '''2001''', ''46'', 3-26]
-  | 2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski001.pdf Lipinski, C. A., Chris Lipinski discusses life and chemistry after the Rule of Five. ''Drug. Discov. Today'' '''2003''', ''8'', 12-6]
+||
+. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Lipinski001.pdf Lipinski, C. A., Chris Lipinski discusses life and chemistry after the Rule of Five. ''Drug. Discov. Today'' '''2003''', ''8'', 12-6]
 |-
-   | <center>2023.12.06 Wed </center>
-  |
+| <center>2024.12.04 Wed </center>
+||
 *''Properties of Known Drugs''
+:1. Drug likeness
+:2. Descriptor-driven design
+||
+. Pak, Steven <br>
-:1 ADME Prediction
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.12.04.AMS535.talk01.pdf pdf]
-:2. QED
+<br> <br>
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.12.06.AMS535.talk01.mp4  Nguyen, An Phuc mp4]
+. Pak, Steven <br>
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.12.06.AMS535.talk01.pdf  pdf]
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.12.06.AMS535.talk02.mp4  Pak, Steven mp4]
+[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2024.12.04.AMS535.talk02.pdf pdf]
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.12.06.AMS535.talk02.pdf  pdf]
+||
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu001.pdf Hou, T. J.; Xu, X. J.; ADME evaluation in drug discovery. ''J. Mol. Model'', '''2002''', ''8'', 337-349]
+:1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Bickerton2012.pdf Bickerton, G. R., Quantifying the chemical beauty of drugs. ''Nature Chemistry'' '''2012''', ''4'', 90-98]
+:2. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/matos_pak_2023.pdf Matos, DRG; Pak, S; Rizzo R; Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit. ''J. Chem. Inf. Model.'' '''2023''']
+||
+|-
-. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/matos_pak_2023.pdf Matos, DRG; Pak, S; Rizzo R; Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit. ''J. Chem. Inf. Model.'' '''2023''']
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/Xu003.pdf Hou, T. J.; Xu, X. J.; AMDE Evaluation in drug discovery 3. Modeling blood-brain barrier partitioning using simple molecular descriptors. ''J. Chem. Inf. Comput. Sci.'', '''2003''', ''43'', 2137-2152]
 |- style="background:lightgreen"
-| <center>-</center>
 ||<center>-</center>
 ||<center>-</center>
-||<center>'''IN CLASS QUIZ for Section 5 2023.12.11 MON'''</center>
 ||<center>-</center>
-|-
+||<center>'''Class Wrap up <br> after <br> QUIZ #5'''</center>
-  | <center>2023.12.11 Mon </center>
+||<center>-</center>
-  |
-:Class Wrap-up
-  | 1. [https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.12.11.AMS535.talk01.mp4  Bickel, John mp4]
-<br>
-[https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2023.12.11.AMS535.talk01.pdf  pdf]
-  |
-  | <center>
 |-
+| <center>2024.12.09 Mon </center>
+||
-|<center>-</center>
+*''Last Day Class''
-||
+||'''QUIZ #5''' <br> <br>
-*'''''Final Exam'''''
 ||<center>-</center>
-||No Final Exam in AMS-535/CHE-535 for Fall 2023
 ||<center>-</center>
 |-