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 |
| 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
|
| 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) |
| 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 Simulation, Emad 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) |
| 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 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.