Computational Biophysics Workshop
Program
Mon, Aug 4: Introduction to Protein Structure and Dynamics - Klaus Schulten
07:30-09:00 | Registration Breakfast |
09:00-09:10 | Opening Remarks |
09:10-10:40 | Structure and Sequence Analysis with VMD |
Coffee Break | |
10:50-12:00 | Introduction to Molecular Dynamics with NAMD |
12:00-12:20 | Q & A |
Lunch Break | |
14:00-16:00 | VMD Tutorial - Using VMD; NAMD Tutorial |
Coffee Break | |
16:15-18:00 | VMD Tutorial - Using VMD; NAMD Tutorial |
Tue, Aug 5: Statistical Mechanics of Proteins - Klaus Schulten
07:30-09:00 | Breakfast |
09:00-10:30 | Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD |
Coffee Break | |
10:50-12:00 | Applications of VMD / NAMD in Modern Research |
12:00-12:30 | Q & A; Group picture |
Lunch Break | |
14:00-16:00 | Participant tutorial options: |
Coffee Break | |
16:15-18:00 | Participant tutorial options: |
Wed, Aug 6: Force Field Parameterization - Emad Tajkhorshid
07:30-09:00 | Breakfast |
09:00-10:30 | Introduction to Topology, Parameters, and Structure Files |
Coffee Break | |
10:50-12:00 | Topology, Parameters, and Structure Files |
12:00-12:20 | Q & A |
Lunch Break | |
14:00-16:00 | Parameterizing a Novel Residue; Topology File Tutorial |
Coffee Break | |
16:15-18:00 | Parameterizing a Novel Residue; Topology File Tutorial - Participant tutorial options: NAMD Tutorial & Stretching Deca-alanine |
Thu, Aug 7: Simulating Membrane Channels - Emad Tajkhorshid
07:30-09:00 | Breakfast |
09:00-10:30 | Introduction and Examples |
Coffee Break | |
10:50-12:00 | Transport in Aquaporins; Nanotubes |
12:00-12:20 | Q & A |
Lunch Break | |
14:00 -16:00 | Membrane Proteins Tutorial; Simulation of Water Permeation through Nanotubes |
Coffee Break | |
16:15-18:00 | Membrane Proteins Tutorial; Simulation of Water Permeation through Nanotubes |
Fri, Aug 8: Introduction to Bioinformatics - Zaida Luthey-Schulten
07:30-09:00 | Breakfast |
09:00-10:30 | Part I - Introduction to Evolutionary Concepts and VMD/MultiSeq Part II - Applications of MultiSeq Evolution of Translation: Dynamics of Recognition in RNA:Protein Complexes |
Coffee Break | |
10:50-12:00 | Part III - Towards in silico Cells: Simulating Processes in Entire Cells |
12:00-12:30 | Q & A; Group picture |
Lunch Break | |
14:00-16:00 | Basic Sequence Analysis: Aquaporins with the VMD MultiSeq
Tool; or |
Coffee Break | |
16:15-18:00 | Basic Sequence Analysis: Aquaporins with the VMD MultiSeq
Tool; or Expert Sequence Analysis - Evolution of Translation Class I Aminoacyl-tRNA Synthetases: tRNA complexes - Evolution of Translation EF-Tu: tRNA - Evolution of Translation: The Ribosome; or, Dynamical Network Analysis, or Participants work on their own projects |
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".