Computational Biophysics Workshop - Pittsburgh, May 21 - 25, 2018

Program

Monday, May 21:
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
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 Servers
15:15-16:00 ProDy API Tutorial - Overview
16:00-16:15 Coffee Break
16:15-18:00 DynOmics Server and ProDy API Applications (Session I):
  1.  GNM analysis of equilibrium dynamics

  2.  ANM analysis of collective motions and visualization by NMWiz

  3.  Ensemble Analysis of Known Structures/Conformer

Tuesday, May 22:
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 ProDy
  • Analysis of ensembles of structures for inferring functional mechanisms
  • Mechanical responses to stress
10:30-10:50 Coffee Break
10:50-12:00
  • Perturbation-Response Scanning
  • Identification of Sensors and Effectors of Allosteric Signals
  • Allosteric Communication Paths
12:00-12:20 Q & A
12:40-14:00 Lunch Break
14:00-16:00 ProDy Tutorial and Applications of ProDy API
16:00-16:15 Coffee Break
16:15-18:00 DynOmics Server and ProDy API Applications (Session II):
  1.  Perturbation response scanning (PRS)

  2.  Evaluation of sites acting as sensors and receptors of signals

  3.  Allosteric communication paths Mechanical stiffness
18:00-19:00 Dinner Break (note: participants are on their own for this meal)
19:00-21:00 Presentations by workshop participants

Wednesday, May 23:

Bridging Sequence, Structure and Function, and Experiments and Computations. Druggability Simulations

Computational Studies of Biomolecular Systems with Molecular Dynamics Simulation

08:30-09:00 Continental Breakfast
09:00-10:30
  • Sequence evolution and co-evolution
  • Druggability simulations
  • Extension of GNM to genome dynamics
  • Hybrid Methods: coMD
  • presented by Ivet Bahar
10:30-10:50 Coffee Break
10:50-12:00 Computational Studies of Biomolecular Systems with Molecular Dynamics Simulation, Emad Tajkhorshid
12:00-12:20 Q & A
12:20-14:00 Lunch Break
14:00-16:00 Suggested Tutorials:
16:00-16:15 Coffee Break
16:15-18:00 Suggested Tutorials:

Thursday, May 24:
Introduction to QwikMD and Parameterization for Classical Force Fields with FFTK

08:30-09:00 Continental Breakfast
09:00-09:30 Introduction to Easy and Fast Simulations with QwikMD, João Ribeiro
09:30-10:30 Introduction to Classical Force Fields - Topology, Parameters, and Structure Files, Emad Tajkhorshid
10:30-10:50 Coffee Break
10:50-12:00 Introduction to Force Field Toolkit, Emad Tajkhorshid
12:00-12:20 Q & A
12:40-14:00 Lunch Break
14:00-16:00 Suggested Tutorials:
16:00-16:15 Coffee Break
16:15-18:00 Suggested Tutorials:
18:30 Group Picture and dinner at Union Grill, S Craig St.

Friday, May 25:
Investigating Biological Membranes and Membrane Proteins in Action Using Advanced Simulation Technologies

08:30-09:00 Continental Breakfast
09:00-10:30 Investigating Biological Membranes and Membrane Proteins in Action Using Advanced Simulation Technologies (Session I), Emad Tajkhorshid
10:30-10:50 Coffee Break
10:50-11:30 Investigating Biological Membranes and Membrane Proteins in Action Using Advanced Simulation Technologies (Session II), Emad Tajkhorshidi
11:30-12:00 Tips and Tricks to Render Images of Biomolecule in VMD, João Ribeiro
12:00-12:20 Q & A
12:40-14:00 Lunch Break
14:00-16:00 Suggested Tutorials:
16:00-16:15 Coffee Break
16:15-18:00 Suggested Tutorials:

 

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 P41GM104601 "Center for Macromolecular Modeling and Bioinformatics", NIH 1R25GM103771 Hands-on Workshops on Computational Biophysics, and NIH P41 GM103712 "NIH Center for Multiscale Modeling of Biological Systems".