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    Molecular Modeling

    G25.2601, Fall 1996, Thursdays 1:20-3:10 pm, 513 WWH

    Course Agenda

    1. Thursday, Sep. 5 (513 WWH)

  • Computer account information
  • What is molecualr modeling and how has it evolved?
  • Two introductory videotape lectures:
    • Gerald Fasman, ``Unlimited Expectations, Limited Applications'', ACS Symposium on Molecular Modeling: Integration of Theory with Experiment; Accuracy of Molecular Modeling, Research Triangle Park, October 1993. (Also brief introduction by Alex Tropsha on the importance of molecular modeling).

    • Peter Kollman, ``Methods in Molecular Modeling'', ACS Interactive Satellite TV Course on Molecular Modeling for Biological Systems, San Diego State University and the San Diego Supercomputer Center, 1990. (Also brief introduction by Sid Karin, SDSC Director, on the growing popularity of molecular modeling).

    Assignment 1 (due Sep. 19): Introduction to the WWW, Sequence and structural databases, and early molecular modeling literature.

    2. Thursday, Sep. 12 (513 WWH)

    • Lecture on the state of molecular modeling today, with an overview of problems, tools, and solution analysis techniques (Lecture Notes 1).

    Assignment 2 (due Sep. 19): Retrieval of structural information from the Protein Data Bank (PDB), and the display, manipulation, and analysis of three-dimensional biomolecular sturctures with the Insight II molecular graphics package.

    3. Thursday, Sep. 19 (122 Meyer)

    • Minitutorials on protein structure (Lecture Notes 2)
    • Begin Minitutorial on nucleic acid structure (Lecture Notes 3).

    Assignment 3 (due Sep. 26): Construction and analysis of an oligopeptide with the Insight II program.

    4. Thursday, Sep. 26(122 Meyer)

    • Discuss homework assignments 1 and 2
    • Minitutorial on nucleic acid structure (Lecture Notes 3).
    • Begin class presentations from homework 1 (early molecualr modeling literature)

    Assignment 4 (due Oct. 10): Generation and analysis of Ramachandran plots for a protein database and introduction to the NDB

    5. Thursday, Oct. 3(313 WWH)

    Guest Lecturer: The Nucleic Acid Database, Prof. Helen Berman, Rutgers University, Department of Chemistry, Developer of NDB

    Assignment 5 (due Oct. 10): Readings: Levitt & Chothia (1976), Lipkowitz (1995), and Cipra (1996)

    6. Thursday, Oct. 10 (513 WWH)

    • Computational and theoretical approaches to structure prediction(from the quantum mechanical to the molecular mechanical description) (Lecture Notes 4).

    Assignment 6 (due Oct. 17): Molecular mechanics force fields: approximations, variations, and the assessment of results with respect to experiment and other simulations.

    7. Thursday, Oct. 17 (513 WWH)

    • Molecular mechanics force fields - origin, variations, and parameterization (Lecture Notes 5).
    • Begin special topics in molecular mechancis - molecular topology: book-keeping and data structures (Lecture Notes 6).

    Assignment 7 (due Oct. 24): A bit of programming: nonbonded versus bonded energy computations. Read on Monte Carlo: Abagyan and Totrov (1994) and from textbooks, such as: (a) malvin Kalos & Paula A. Whitlock (1986) : Monte Carlo Methods, John Wiley & Sons, New York, and (b) Paul Bratley, Bennet L. Fox, & Linus E. Schrage (1987): A Guide to Simulation , Springer-Verlag, New York.

    8. Thursday, Oct. 24

  • Guest Lecturer: Protein Struture Prediction by Global Energy Optimization. Prof. Ruben Abagyan, Skirball Institute of Medicine, NYU Medical Center (Abagyan Lecture Notes).
  • Assignment : NONE. Term project announced.

    9. Thursday, Oct. 31

  • Guest Lecturer: Monte Carlo Methodology, Prof. Jonathan Goodman, Courant Institute of Mathematical Sciences, NYU (Goodman Lecture Notes).
  • Assignment: Continue work on Assignment 7 ... (programming).

    10. Thursday, Nov. 7(513 WWH)

    • Go over Assignment 7, including general discussion of programming and timeing strategies (Notes on Assignment 7).
    • Continue special topics in molecular mechanics - potential energy differentian (Lecture Notes 7).
    • Begin special issues in nonbonded energy computations - spherical cutoffs (Lecture Notes 8).

    Assignment 8 TERM PROJECT (due Dec. 15): The Successes (failures?) of Molecular Modeling.

    11. Thursday, Nov. 14 (513 WWH)

    • Continue special issues in nonbonded energy computations - spherical cutoffs, fast electrostatics by the multipole method, periodic boundary conditions, and the Ewald summation (Lecture Notes 8).

    Assignment 9 (due Dec. 5): TBA. Experiments in Geometry Structure Optimization: Minimization of Biphenyl with Insight II/Discover. Read Schlick (1992) on optimization methods in computational chemistry and the CSEP chapter on mathematical optimization by T. Schlick and G. Parks

    12. Thursday, Nov. 21(513 WWH)

  • The Force Field Debate!
  • Assignment 10 (due Dec. 5): A Global Optimization Contest for a Pentapeptide!

    13. Thursday, Nov. 28


    14. Thursday, Dec. 5(513 WWH)

    • Optimization techniques for multivariate functions in computational chemistry (Lecture Notes 9).

    Assignment (due Dec. 12): Read Scheraga (1992).

    15. Thursday, Dec. 12(513 WWH)

    Guest Lecturer: Computational Approaches to the Multiple Minima Problem, Prof. Harold Scheraga, Cornell University.

    Assignment TERM PROJECT due Dec. 15.

    16. Friday, Dec. 13

    EXAM DAY (Class Schedual - Discussion, Lecture, Etc. - TBA)!

    • Tenative: Begin molecular dynamics - theory and practice (Lecture Notes 10).

    Monday, Dec. 15 TERM PROJECT DUE!

    Updated 11/11/96