Agenda: Hands-on Workshop on Computational Biophysics 2018
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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 | |
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Collective Dynamics of Proteins Using Elastic Network Models. From single molecules to biological assemblies |
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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 |
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
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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 |
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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:
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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 |
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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.