Agenda: Hands-on Workshop on Computational Biophysics 2017

 

Application decisions have been finalized. Please check your email.

 

Agenda

The tentative agenda, subject to change, is as follows:

 

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
10:30-10:50 Coffee Break 
10:50-12:00 Applications to Biological Assemblies: Gaussian Network Model (GNM)
12:00-12:20 Q & A
12:20-13:45 Lunch Break 
13:45-15:15 GNM,  ANM and DynOmics and ANM Servers
15:15 - 16:00 ProDy Tutorial  - Overview
16:00-16:15 Coffee Break 
16:15-18:00

ProDy Modules

  1. Structural analysis
  2. GNM analysis of equilibrium dynamics
  3. ANM analysis of collective motions and visualization by NMWiz
  4. Ensemble Analysis of Known Structures/Conformer
  5. Perturbation response scanning (PRS) 
  6. Evaluation of sites acting as sensors and receptors of signals 
  7. Allosteric communication paths
   
   
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 Introduction to ProDy API
Analysis of ensembles of structures for inferring functional mechanisms
Mechanical responses to stress
10:30-10:50 Coffee Break 
10:50-12:00 Sequence evolution and co-evolution
Druggability simulations
Extension of GNM to genome dynamics
12:0-12:20 Q & A
12:20-14:00 Lunch Break 
14:00-16:00 ProDy Tutorial and Applications  
16:00-16:15 Coffee Break 
16:15-18:00

ProDy Modules

  1. Mechanical stiffness
  2. Druggability simulations
  3. Evol analysis for sequence conservation and co-evolution
18:00-19:00 Dinner Break (note: participants are on their own for this meal)
19:00-21:00 Presentations by workshop participants
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
10:30-10:50 Coffee Break
10:50-12:00 Applications of Molecular Dynamics with NAMD
12:00-12:20 Q & A; group picture
12:20-14:00 Lunch Break 
14:00-16:00 VMD Tutorial; QwikMD Tutorial; NAMD Tutorial
16:00-16:15 Coffee Break 
16:15-18:00 VMD Tutorial; QwikMD Tutorial; NAMD Tutorial
18:30 Group dinner at Union Grill, S Craig St.
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
10:30-10:50 Coffee Break
10:50-12:00 Introduction to Force Field Toolkit
12:00-12:30 Q & A
12:30-14:00 Lunch Break 
14:00-16:00

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

Participant tutorial options:
1) Parameterizing Small Molecules Using Force Field Toolkit
2) Parameterizing a Novel Residue
3) Topology File Tutorial

Tutorials

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

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