Computational Biophysics Workshop - Pittsburgh, May 30 - June 2, 2017

Program

Tuesday, May 30:
Collective Dynamics of Proteins Using Elastic Network Models. From single molecules to biological assemblies
Ivet Bahar

08:00-08:30 Registration and Continental Breakfast
08:30-09:00 Welcome and Brief Overview - Ivet Bahar
09:00-09:10 Opening Remarks
09:10-10:30 Elastic Network Models (ENMs) and Collective Motions. Basic Theory and Methods
Coffee Break  
10:50-12:00 Applications to Biological Assemblies: Gaussian Network Model (GNM)
12:00-12:20 Q & A
Lunch Break  
14:00-16:00 GNM and ANM
Coffee Break  
16:15-18:00

Participant tutorial options:
1) Mean-square fluctuation profiles
2) Cross-correlations
3) Cooperative conformational changes along selected modes
4) Evaluation of sites acting as sensors and receptors of signals
5) Allosteric communication paths
6) Estimation of functional sites

Wednesday, May 31:
Bridging Sequence, Structure and Function, and Experiments and Computations. Druggability Simulations
Ivet Bahar

08:30-09:00 Continental Breakfast
09:00-10:30 EAnalysis of ensembles of structures for inferring functional mechanisms. Introduction to ProDy API ProDy
Coffee Break  
10:50-12:00 Sequence evolution and co-evolution. Structural mechanics. Hybrid methods combining MD and ANM for efficient exploration of conformational space. Druggability simulations
12:0-12:20 Q & A
Lunch Break  
14:00-16:00 ProDy Tutorial and Applications of ProDy API (http://prody.csb.pitt.edu/)
Coffee Break  
16:15-18:00

Participant tutorial options:
1) ENM Analysis
2) Ensemble Analysiss
3) Mechanical Stiffness
4) Druggability Simulations
5) Evol Analysis for sequence conservation and co-evolution

Thursday, June 1:
Principles and Applications of Molecular Dynamics Simulations with NAMD, VMD & QwikMD
Emad Tajkhorshid

08:30-09:00 Continental Breakfast
09:00-10:30 Introduction to Molecular Dynamics with NAMD, VMD & QwikMD
Coffee Break  
10:50-12:00 Applications of Molecular Dynamics with NAMD
12:00-12:20 Q & A
Lunch Break  
14:00-16:00 VMD Tutorial; QwikMD Tutorial; NAMD Tutorial
Coffee Break  
16:15-18:00 VMD Tutorial; QwikMD Tutorial; NAMD Tutorial

Friday, June 2:
Parameterization for Classical Force Fields with FFTK
Emad Tajkhorshid

08:30-09:00 Continental Breakfast
09:00-10:30 Introduction to Classical Force Fields - Topology, Parameters, and Structure Files
Coffee Break  
10:50-12:00 Introduction to Force Field Toolkit
12:00-12:30 Q & A; Group picture
Lunch Break  
14:00-16:00

Participant tutorial options:
1) Parameterizing Small Molecules Using Force Field Toolkit, or
2) Parameterizing a Novel Residue, or
3) Topology File Tutorial
Coffee Break  
16:15-18:00

Participant tutorial options:
1) Parameterizing Small Molecules Using Force Field Toolkit, or
2) Parameterizing a Novel Residue, or
3) Topology File Tutorial
Dinner Break (note: participants are on their own for this meal)
19:00-21:00 Presentations by workshop participants

 

Click here to see descriptions of tutorials listed in program.

Note: participants may also download and get assistance with other tutorials from the TCBG tutorials website during the workshop.

Program subject to change. Workshop supported by NIH 9P41GM104601 "Center for Macromolecular Modeling and Bioinformatics", and NIH P41 GM103712 "NIH Center for Multiscale Modeling of Biological Systems".