Computational Biophysics Workshop - Urbana, Oct. 22-26, 2012

Program

Locations:
  • Lectures: Room 3269 of the Beckman Institute
  • Tutorials: Room 3269 and TCBG Innovation Areas I & II at Beckman

Mon, Oct. 22: Introduction to Protein Structure and Dynamics - Klaus Schulten

08:30-09:00 Registration
09:00-09:10 Opening Remarks
09:10-10:40 Structure and Sequence Analysis with VMD
Coffee Break  
11:00-12:00 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
Dinner Break  
19:30-20:00 VMD from the Developer's Perspective - John Stone
20:00-20:30 Computational Investigation of DNA Detection Using Graphene Nanopores - Chaitanya Sathe
20:30-21:00 Workshop Participant Short Lecture: Atomistic Molecular Dynamics Simulation of Poliovirus - Jason Roberts

 

Tue, Oct. 23: Introduction to Bioinformatics - Zaida Luthey-Schulten

09:00-10:30 Introduction to Evolutionary Concepts in Bioinformatics: MultiSeq in VMD
Coffee Break  
10:50-12:00 Application of MultiSeq to Evolution of Translation Machinery
12:00-12:20 Q & A
Lunch Break  
14:00-16:00

Participant tutorial options:
1) Basic Sequence Analysis: Aquaporins with the VMD MultiSeq Tool; or
2) 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
3) Dynamical Network Analysis
4) Participants work on their own projects

Coffee Break  
16:15-18:00

Participant tutorial options:
1) Basic Sequence Analysis: Aquaporins with the VMD MultiSeq Tool; or
2) 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
3) Dynamical Network Analysis
4) Participants work on their own projects

Dinner Break  
19:30-20:00 NAMD from the Developer's Perspective - Jim Phillips
20:00-20:30 Molecular Dynamics Simulation of Protein Folding - Yanxin Liu
20:30-21:00

Workshop Participant Short Lectures:
• Construction, Validation and Testing of a Novel Comprehensive Pharmacophore Model for Anthrax Toxin Lethal Factor Inhibitors - Ting-Lan Chiu
• Modelling Osmotic Stress Effects on Macromolecules - Ajith Rajapaksha

21:00-21:30 Cloud Computing Opportunities for Computational Investigators (Amazon) - Ryan McGreevy

 

Wed, Oct. 24: Statistical Mechanics of Proteins - Klaus Schulten

09:00-10:00 Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD
10:00-10:45 Applications of VMD / NAMD in Modern Research
Coffee Break  
11:00-12:00 Introduction to GPU Accelerated NAMD Simulation - K. Schulten, R. McGreevy
12:00-12:30 Q & A; Group picture
Lunch Break  
14:00-16:00 Participant tutorial options:
1) NAMD Tutorial & Stretching Deca-alanine, or
2) Expert NAMD Set Tutorials*, or
3) Free Energy Set Tutorials**
4) GPU Accelerated Molecular Dynamics and Visualization Tutorial
Coffee Break  
16:15-18:00 Participant tutorial options:
1) NAMD Tutorial & Stretching Deca-alanine, or
2) Expert NAMD Set Tutorials*, or
3) Free Energy Set Tutorials**
4) GPU Accelerated Molecular Dynamics and Visualization Tutorial

 

Thu, Oct. 25: Parameters for Classical Force Fields - Emad Tajkhorshid

09:00-10:30 Introduction to Topology, Parameters, and Structure Files
Coffee Break  
10:50-12:00 Examples and Applications
12:00-12:20 Q & A
Lunch Break  
14:00-16:30 Parameterizing a Novel Residue
Coffee Break  
16:45-18:00 Topology File Tutorial
Dinner Break  
20:00-20:30 Molecular Dynamics Flexible Fitting - Ryan McGreevy
20:30-21:00 Structural Analyses of the Ribosome by Hybrid Approach - Yan Chan
21:00-21:30 Workshop Participant Short Lecture: Deprotonation of D96 in Bacteriorhodopsin Opens the Proton Uptake Pathway - Ting Wang

 

Fri, Oct. 26: Simulating Membrane Channels - Emad Tajkhorshid

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 Participant tutorial options:
1) Membrane Proteins & Simulation of Water Permeation Through Nanotubes, or
2) Expert NAMD Set Tutorials*, or
3) Free Energy Set Tutorials**
Coffee Break  
16:15-18:00 Participant tutorial options:
1) Membrane Proteins & Simulation of Water Permeation Through Nanotubes, or
2) Expert NAMD Set Tutorials*, or
3) Free Energy Set Tutorials**
Dinner Break  
20:00-21:30

Final Presentations by Workshop Participants:
• Structural Basis for the Cooperativity between Heterogenous Subunits of Group II Chaperonin - Kai Zhang
• Applying the Stochastic Liouville Equation to Light-Harvesting Complexes - Albrecht Goez
• The Effect of Hydroxyl Groups on Thermodynamics of Ligand-Protein Binding for the Phenyl based Ligands - Oleg Starovoytov
• Computational Studies of Sodium Dodecyl Sulfate - Anne Laustsen

 

Tutorial Options:
* Expert NAMD Set Tutorials:
     - Shape-Based Coarse Graining
     - User-Defined Forces in NAMD, or
** Free Energy Set Tutorials
     - A Tutorial to Set Up Alchemical Free Energy Perturbation Calculations in NAMD
     - A Tutorial to Set Up Adaptive Biasing Force Calculations in NAMD

Click here to see descriptions of tutorials listed in program.

Note: program subject to change. Workshop supported by NIH P41-RR005969 "Resource for Macromolecular Modeling and Bioinformatics".