Agenda: Hands-on Workshop on Computational Biophysics 2018

Apply  |   Home   |  Agenda  |   Instructors   | Google Maps

Application Deadline: April 15 2018

 

 Presentations from prior workshops are available on the MMBioS YouTube channel.

Agenda

This agenda is tentative and subject to change. 

 

Monday, May 21
Collective Dynamics of Proteins Using Elastic Network Models. From single molecules to biological assemblies
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, Ivet Bahar
10:30-10:50 Coffee Break 
10:50-12:00

Applications to Biological Assemblies: Gaussian Network Model (GNM), Ivet Bahar

GNMANM and DynOmicsIvet Bahar

12:00-12:20 Q & A
12:20-14:00 Lunch Break 
14:00-15:45 ProDy Tutorial  - Overview, She (John) Zhang
15:45-16:00 Coffee Break 
16:00-17:45 DynOmics Server and ProDy API Applications: Session I
  1. GNM analysis of equilibrium dynamics (Luca Ponzoni)
  2. ANM analysis of collective motions and visualization by NMWIz (James Krieger
Tuesday May 22
Bridging Structure and Function, and Experiments and Computations. Perturbation-response scanning and mechanical responses
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, Ivet Bahar
10:30-10:50 Coffee Break 
10:50-12:00 Perturbation-Response Scanning
Identification of Sensors and Effectors of Allosteric Signals
Allosteric Communication paths, Ivet Bahar
12:00-12:20 Q & A
12:20-14:00 Lunch Break 
14:00-15:45 Ensemble analysis of known structures/conformer (Karolina Mikulska- Ruminska)
Mechanical stiffness (Karolina Mikulska- Ruminska)
15:45-16:00 Coffee Break 
16:00-17:45

Evaluation of sites acting as sensors and effectors of allosteric signals (James Kreiger)

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. Druggability Simulations.
Computational Studies of Biomolecular Systems with Molecular Dynamics Simulations
08:30-09:00 Continental Breakfast
09:00-10:30 Sequence evolution and co-evolution
Druggability simulations, 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 
14:00-15:45 Suggested Tutorials:
15:45-16:00 Coffee Break 
16:00-17:45 Suggested Tutorials:
Thursday May 24
Introduction to QwikMD and Parameterization for Classical Force Fields with FFTK
08:30-09:00 Continental Breakfast
09:00-9:30 Introduction to Easy and Fast Simulations with QwikMD, João Ribero
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 and Group Picture
12:20-14:00 Lunch Break 
14:00-16:00 Suggested tutorials:
16:00-16:15 Coffee Break 
16:15-18:00 Suggested tutorials:
18:30 Dinner at Legume,  214 N Craig St.
Friday May 25
Investigating Biological Membranes and Membrane Proteins in Action Using Advanced Simulation Techniques
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 Tajkhorshid
11:30-12:00 Tips and Tricks to Render Images of Biomolecules in VMD, João Ribero
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:

 

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 the Theoretical and Computational Biophysics group, NIH Center for Macromolecular Modeling and Bioinformatics, at the Beckman Institute, University of Illinois at Urbana-Champaign and the NIH Center for Multiscale Modeling of Biological Systems.

Copyright © 2020 National Center for Multiscale Modeling of Biological Systems. All Rights Reserved.