Molecular Modeling, Syllabus

MOLECULAR MODELING
Chemistry: G25.2601
Biology: G23.2601
Mathematics: G63.2856.003
Computer Science: G22.3033.11
Sackler: G16.2607
SYLLABUS

Agenda

Schedule

Syllabus

Books

Articles

InsightII

Spartan

Kinemage

Related Sites

Professor Information

Instructor

Assistants

Students

Computer

Email List

SCIVIS Accounts

Table1: Syllabus 1999
Class
Date Subject Homework
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.

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

Class	Date	Subject	Homework
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.
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