Agenda: Hands-on Workshop on Computational Biophysics 2019

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

Agenda

This agenda is tentative and subject to change. 

 

Monday, May 13
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
Gaussian Network Model (GNM), Anisotropic Network Model (ANM), Ivet Bahar
10:30-10:50 Coffee Break 
10:50-12:00

Applications to Biological Assemblies: Gaussian Network Model (GNM), Ivet Bahar
Use of iGNM DB, ANM server, and DynOmics server
Introduction to ProDy APIIvet Bahar

12:00-12:20 Q & A
12:20-14:00 Lunch Break 
14:00-15:45 ProDy API Applications: Session I
Basics and Tutorials [notebook] -  (John Zhang)
15:45-16:00 Coffee Break 
16:00-17:45 ProDy API Applications: Session II
  1. GNM Analysis of Equilibrium Dynamics [notebook] (Burak Kaynak)
  2. ANM Analysis of Collective Motions and Visualization by NMWiz [notebook] (Yan Zhang
Tuesday May 14
Bridging Sequence, Structure and Function, and Experiments and Computations. Signature dynamics of families and Allosteric Signaling
08:30-09:00 Continental Breakfast
09:00-10:30 ProDy Analysis of Ensembles of Structures for Inferring Functional Mechanisms
Evol: Bridging Sequence and Structure, Pemra Doruker
10:30-10:50 Coffee Break 
10:50-12:00 Signature Dynamics of Protein Families
Perturbation-Response Scanning
Identification of Sensors and Effectors of Allosteric Signals, Pemra Doruker
12:00-12:20 Q & A
12:20-14:00 Lunch Break 
14:00-15:45 Ensemble analysis using ProDy [notebook] (John Zhang)
Evol: Sequence Conservation and Evolution [notebook] (Luca Ponzoni)
15:45-16:00 Coffee Break 
16:00-17:45

SignDy: Signature Dynamics of Protein Families [notebook] (James Krieger & Hongchun Li)
Evaluation of Sites Acting as Sensors and Effectors of Allosteric Signals [notebook] (James Krieger)

18:00-19:00 Dinner Break (note: participants are on their own for this meal)
19:00-21:00 Presentations by workshop participants (optional)
Wednesday May 15
Modeling and Simulations of Environmental Effects, Membrane Proteins and Druggability ; Introduction to MD Simulations Using NAMD
08:30-09:00 Continental Breakfast
09:00-10:30 Modeling the Dynamics of System & Environment using Elastic Network Models
Membrane Proteins using ENMs for Lipid Bilayer
Druggability Simulations, Ivet Bahar
10:30-10:50 Coffee Break
10:50-12:00 Computational Studies of Biomolecular Systems with Molecular Dynamics SimulationEmad Tajkhorshid
12:00-12:20 Q & A
12:20-14:00 Lunch Break 
14:00-15:45

Membrane Proteins and Environmental Effects [notebook] (John Zhang and Hongchun Li)
Druggability (link is 865MB) (Jiyoung Lee)

15:45-16:00 Coffee Break 
16:00-17:45 Suggested Tutorials:
Thursday May 16
Introduction to QwikMD and Parameterization for Classical Force Fields with FFTK
08:30-09:00 Continental Breakfast
09:00-10:30 Molecular Dynamics Simulations with NAMD and VMD, João Ribero
10:30-10:50 Coffee Break
10:50-11:30 Easy and Fast Simulations with QwikMD, João Ribero
11:30-12:00 Introduction to Force Field Toolkit, Mariano/Soumyo
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 Group Dinner at Lucca,  317 S Craig St.
Friday May 17
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 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 IIEmad 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.

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