CS6104: Structural Bioinformatics and Computational Biophysics - Spring 2004

TUE 3.30 - 6.00 pm WILLIAMS 334


"Everything that the living things do ... can be described as the wiggling and jiggling of atoms" R. Feynman


Instructor:        Alexey Onufriev
Office:              2160C Torgersen Hall
Phone:              (540)231-4237 (E-mail is strongly preferred)
Email:               onufriev@cs.vt.edu
Office Hours:    Tue 1-3pm
Text Books:
Syllabus:

First Day Handout

Computer Labs available

Class Picture. May 2004.


Classes:

Date Topic Presenter
Jan 20 Introduction Alexey
Jan 27 Projects Alexey
Feb 03 PBD Formate Completion II
Feb 10 1. DNA Background
2. Protein Structure
DNA
Hinges
Feb 17 1. Protein - pK and Ligand Binding
2. Ligand Binding
3. Molecular Visualization
Completion I
Potential Maps
Myoglobin
Feb 24 1. Molecular Dynamics Simulations
2. Molecular Volume and Surface
3. Protein Structure and Function
4. Progress Reports
Alexey
Fast Volume
Graphs
-
Mar 02 RNA Folding
Topomer Search Model
Completion II
Hinges
Mar 09 Spring Break -
Mar 16 1. Nucleic Acid Builder
2. Fuzzy Functional Forms
DNA
Graphs
Mar 23 Canceled -
Mar 30 1. Monte Carlo Methods
2. MSMS
3. Protein Folding
Competation I
John
Hinges
Apr 06 Homology Modeling & Molecular Docking Dr.Bevan
Apr 13 1. Seminar: Sequence Assembly and Protein Docking Algorithms
2. Progess Reports
Vicky Choi
-
Apr 20 1. Seminar: Surface Complementarity in Molecular Recognition
2. Progress Reports
Vladimir Sobolev
-
Apr 27 1. Computation in Drug Design
2. Drug Design from Structure
3. Packing in Spheres
-
-
Potential Maps
May 04 - -
May 11 - -


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