Molecular Modeling Course 99

A New Spring' 99 Offering


Course Information
Related Sites
General Information
Professor Information
Email List
SCIVIS Accounts
Chemistry: G25.2601
Biology: G23.2601
Mathematics: G63.2856.003
Computer Science: G22.3033.11
Sackler: G16.2607

Time: Thursdays, 12:45-2:45pm

Location: 1003 Main Building

Table1: Schedule 1999
Class Date Subject Homeworka
1 1/21 Course and Field Overview:
  • What is molecular modeling and how has it evoled?

  • What are the practical applications and important questions?
1: Introduction to web browing and searching, sequence and structural databases, and early molecular modeling literature.
Read papers 1,2,19,32.
2 1/28
  • Continuation of the overview on biomolecular modeling and simulation, from drug design to new materials
  • Discussion of the 1959 paper of Alder and Wainwight: difficulties then and now
  • Introduction ot interesting biomolecular modeling problems: protein folding, protein misfolding, nucleic acid/protein interactions, and RNA folding (Transparency Set 1 and Lecture Notes 1 [preface and Chapter1])
2: Retrieval of structural information from the Protein Data Bank (PDB), an the display, manipulation, and analysis of three-dimensional biomolecular structures with the Insight II molecular graphics package. Explore kinemage tutorials.
Read papers 4, 29, 30, 33.
3 2/4
  • Minitutorial on protein structure: aminoacid repertoire, primary to quaternary structure, protein structure classification
  • Kinemage tutorial demonstration: folding motifs and major protein classes
3: Construction and analysis of the pentapeptide Met-enkephalin with the InsightII program.
Read papers 2, 3, 5.
4 2/11
  • Discuss homework assingments 1 and 2
  • Minitutorial on nucleic acid structure: building blocks, backbone confirmational
4: Generation and analysis of Ramachandran plots for proteins and introduction to the NDB
Read papers 22,28
5 2/18 Guest Lecturer: The Nucleic Acid Database and the 'New Protein Databank' (RCSB), Prof. Helen Berman (Rutgers university, Department of Chemistry), Director of NDB and RCSB 5: Analysis of Protein/DNA Complexes with Insight and NDB
Read papers 6,20
6 2/25
  • Discuss homework assignment 4
  • Computational and theoretical approaches to structure prediction (from the quantum-mechanical to the molecular mechanical description) (Transp. 4 and Lecture Notes 5)
6: (MIDTERM): Sequence/Structure/Function Relationships in Protein, A Contest (Due 3/15)
Read paper 21
7 3/1 Guest Lecture: Biomolecular Electrostatics and NMR Refinement, Dr. Dave Case (Scripps Institute, Department of Molecular Biology), a developer of AMBER and expert in biomolecular simulations 7: Molecular mechanics force fields: approximations, variations, and the assessment of results with respect to experiment and other simulations
Read papers 12,13,16,23
8 3/5 Amer. Chem. Soc. 1990 videotapes: Molecular Modeling in Biological Systems: 1-Peter Kollman, "Methods in molecular Modeling", 4-Panel Discussion.
9 3/11 Guest Lecturer: Computation of Protein Conformation, Prof. Harold Scheraga (Cornell University, Department of Chemistry), pioneer of protein force fields and computation of protein structure 8: A bit of programming: nonbonded versus bonded energy computations.
bReading list
10 3/25
    MIDTERM class presentatins
11 4/1
  • Continue Midterm presentations
  • Force Field Debate!
The Successes (failures?) of Molecular Modeling
Reading papers 9,17,18
12 4/8
  • Molecular mechanics force fields--origin, variations, and parameterization
  • Special topics -- molecular topology: book-keeping and data structures, potential energy differentiation
  • (Transp. Notes 5,6,7)
  • Special issues in nonbonded energy computations--spherical cutoffs, fast electrostatics by the multipole method, periodic boundary condictions, and the Ewald summation (Transp. Notes 8)
10: Experiments in Geometry Structure Optimization: Minimizaton of Biphenyl with InsightII/Discover.
Reading papers 11.
13 4/15
  • Go over Assignment 8, including general discussion of programming and timing strategies
    (Notes on Assignment 8)
  • Optimization techniques for multivariate functions in computational chemistry
    (Transp. Notes 9)
11: A global optimization contest for a pentapeptide!
Reading papers 24,25.
14 4/22 Monte Carlo Simulations 12: An exercise in Monte Carlo
Reading papers 26,27,31.
15 4/29 Molecular dynamics simulations-theory and practice
16 ?? Molecular dynamics simulatons - continued (Transp. Notes 10) TERM PROJECT DUE
aArticle numbers refer to items in the course reading list.
bReading list for Professor Scheraga.

For further information, contact T. Schlick by email ( phone (998-3116) or fax (995-4152).