Details: Published: Friday, 24 June 2022 14:18

Agenda: Hands-on Workshop on Computational Biophysics 2022

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

Agenda

This agenda is tentative and subject to change.

Tuesday, July 5
*Collective Dynamics of Proteins Using Elastic Network Models. From Single Molecules to Biological assemblies*
10:30-11:00	Welcome and Brief Overview, Ivet Bahar
11:00-12:20	Elastic Network Models (ENMs) and Collective Motions. Basic Theory and Methods, Ivet Bahar
12:20-12:40	Break / Social
12:40-2:00	Bridging structure and function, theory and experiments, Ivet Bahar Ensemble Analysis of Structures for Inferring Functional Mechanisms, DynOmics Server, Ivet Bahar
2:00-2:20	Q & A
2:20-3:00	Lunch / Dinner Break
3:00-4:30	ProDy API Basics, Anupam Banerjee GNM Analysis of Equilibrium Dynamics, Frank Zhang
4:30-4:50	Break / Social
4:50-6:45	ANM Analysis of Collective Motions and Visualization by NMWiz, Jiyoung Lee Ensemble Analysis by ProDy, Zak Dahmani
*Note that schedule is in Eastern Time
Wednesday, July 6
Bridging Sequence, Structure and Function, and Experiments and Computations. Signature Dynamics of Protein Families and Allosteric Signaling. Modeling and Simulations of Environmental Effects, Membrane Proteins, and Druggability
10:30-11:00	Social
11:00-12:20	Evol: Bridging Sequence and Structure, Signature Dynamics of Protein Families, ENM for Membrane Proteins, Ivet Bahar
12:20-12:40	Break / Social
12:40-2:00	Allostery and Druggability Simulations, Ivet Bahar
2:00-2:20	Q & A
2:20-3:00	Lunch/ Dinner Break
3:00-4:30	Evol and SignDy, Anupam Banerjee Membrane ANM, Zak Dahmani
4:30-4:50	Break / Social
4:50-6:45	ESSA, Anupam Banerjee Druggability Suite, Jiyoung Lee
*Note that schedule is in Eastern Time
Thursday, July 7
*Molecular Simulation and Visualization with NAMD and VMD*
10:30-11:00	Breakfast / Social
11:00-12:20	Introduction to Biomolecular Simulation, Emad Tajkhorshid Molecular Modeling, Visualization, and Analysis in VMD, Barry Isralewitz and Mariano Spivak
12:20-12:40	Break / Social
12:40-2:00	Quick setup and analysis of NAMD simulations with QwikMD, Rafael Bernardi Ab initio protein structure modeling with Alphafold in VMD, Rafael Bernardi
2:00-2:20	Q & A
2:20-3:00	Lunch Break / Social
3:00-4:30	Tutorial session I QwikMD Tutorial NAMD Tutorial VMD Tutorial
4:30-4:50	Tutorial Progress Q & A / Snack Break / Social
4:50-6:45	Tutorial session II QwikMD Tutorial (cont.) NAMD Tutorial (cont.) VMD Tutorial (cont.)
*Note that schedule is in Eastern Time
Friday, July 8
*Introduction to Advanced Simulation Techniques, Collective Variables and QwikMD*
10:30-11:00	Breakfast / Social
11:00-12:20	Battling the Timescale in Classical MD Simulations - Introduction to Enhanced Sampling and Non-equilibrium methods, Emad Tajkhorshid Collective variables, Jérôme Henin
12:20-12:40	Break / Social
12:40-2:00	NAMD Features and Capabilities, David Hardy and Mohammad S. Barhaghi Modeling and Parametrization of Small Molecules with Molefacture and Force-Field Toolkit, Mariano Spivak
2:00-2:20	Q & A
2:20-3:00	Lunch Break
3:00-4:30	Tutorial session I Free Energy Tutorial Colvar Tutorial FFTK Tutorial
4:30-4:50	Break / Social
4:50-6:45	Tutorial session II Free Energy Tutorial Colvar Tutorial FFTK Tutorial
*Note that schedule is in Eastern Time

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.