Computational Biophysics Workshop - Berkeley, August 3-7, 2015
Program
Location
Room 115, Energy Biosciences Building
University of California Berkeley
2151 Berkeley Way, Berkeley, CA 94704
Monday, August 3:
Introduction to Protein Structure and Dynamics - Klaus Schulten
08:00-08:30 |
Registration and Continental Breakfast |
08:30-09:00 |
Welcome, Brief Overview, and Opening Remarks |
09:00-10:30 |
Structure and Sequence Analysis with VMD |
10:30-10:50 |
Coffee Break |
10:50-12:00 |
Introduction to Molecular Dynamics with NAMD |
12:00-12:20 |
Q & A |
12:20-13:30 |
Lunch Break |
13:30-15:30 |
Tutorials |
15:30-15:50 |
Coffee Break |
15:50-17:00 |
Tutorials |
Recommended tutorials: |
VMD Tutorial, NAMD Tutorial |
Tuesday, August 4:
Statistical Mechanics of Proteins - Klaus Schulten
08:00-08:30 |
Continental Breakfast |
08:30-10:00 |
Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD |
10:00-10:20 |
Coffee Break |
10:20-11:30 |
Applications of VMD / NAMD in Modern Research |
11:30-11:50 |
Q & A; Group Picture |
11:50-13:00 |
Lunch Break |
13:00-15:00 |
Tutorials |
15:00-15:20 |
Coffee Break |
15:20-17:00 |
Tutorials |
Recommended tutorials: |
NAMD Tutorial & Stretching Deca-alanine, User-Defined Forces in NAMD
|
Wednesday, August 5:
Force Field Parameterization - Emad Tajkhorshid
08:00-08:30 |
Continental Breakfast |
08:30-10:00 |
Introduction to Classical Force Fields - Topology, Parameters, and Structure Files |
10:00-10:20 |
Coffee Break |
10:20-11:30 |
Examples and Applications / Force Field Toolkit |
11:30-11:50 |
Q & A |
11:50-13:00 |
Lunch Break |
13:00-15:00 |
Tutorials |
15:00-15:20 |
Coffee Break |
15:20-17:00 |
Tutorials |
Recommended tutorials: |
Topology File Tutorial, Parametrizing a Novel Residue Tutorial |
Thursday, August 6:
Molecular Dynamics Flexible Fitting Methods - Ryan McGreevy
08:00-08:30 |
Continental Breakfast |
08:30-10:00 |
Molecular Dynamics Flexible Fitting Method I |
10:00-10:20 |
Coffee Break |
10:20-11:30 |
Molecular Dynamics Flexible Fitting Method II |
11:30-11:50 |
Q & A |
11:50-13:00 |
Lunch Break |
13:00-15:00 |
Tutorials |
15:00-15:20 |
Coffee Break |
15:20-17:00 |
Tutorials |
Recommended tutorials: |
MDFF Tutorial, Structure check Tutorial |
Friday, August 7:
Introductions to Evolutionary Concepts, Network Analysis, and Cell Simulations - Zan Luthey-Schulten
08:00-08:30 |
Continental Breakfast |
08:30-10:00 |
Applications of Evolutionary Algorithms and Network Analysis in MultiSeq/VMD to Translation |
10:00-10:20 |
Coffee Break |
10:20-11:30 |
Introduction to Simulations of Bacterial Cells |
11:30-11:50 |
Q & A |
11:50-13:00 |
Lunch Break |
13:00-15:00 |
Tutorials |
15:00-15:20 |
Coffee Break |
15:20-17:00 |
Tutorials |
Recommended tutorials: |
Lattice Microbe Simulations. Other tutorials of interest: Aquaporins with the VMD MultiSeq Tool, Evolution of Translation: Class-I aminoacyl-tRNA synthetases, Evolution of Translation: EF-Tu, Evolution of Translation: Ribosome, Dynamical Network Analysis |
Click here to see descriptions of tutorials listed in program.
Note: program subject to change. Workshop supported by NIH 9P41GM104601 "Center for Macromolecular Modeling and Bioinformatics".