Agenda: Hands-on Workshop on Computational Biophysics 2021

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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, June 28
*Collective Dynamics of Proteins Using Elastic Network Models. From Single Molecules to Biological assemblies*
9:00-10:30	Welcome and Brief Overview, Ivet Bahar
10:00-11:20	Elastic Network Models (ENMs) and Collective Motions. Basic Theory and Methods, Ivet Bahar
11:20-11:40	Break / Social
11:40-1:00	Bridging structure and function, theory and experiments, Ivet Bahar Ensemble Analysis of Structures for Inferring Functional Mechanisms, DynOmics Server, Pemra Doruker
1:00-1:20	Q & A
1:20-2:00	Lunch / Dinner Break
2:00-3:30	ProDy API Basics, Burak Kaynak GNM Analysis of Equilibrium Dynamics, Burak Kaynak
3:30-3:50	Break / Social
3:50-5:45	ANM Analysis of Collective Motions and Visualization by NMWiz, Burak Kaynak Ensemble Analysis by ProDy, Bentley Wingert
*Note that schedule is in Central Daylight time
Tuesday, June 29
*Bridging Sequence, Structure and Function; Signature Dynamics of Protein Families; Allosteric Signaling; Modeling and Simulations of Environmental Effects; Membrane Proteins; and Druggability*
9:30-10:00	Social
10:00-11:20	Evol: Bridging Sequence and Structure, Signature Dynamics of Protein Families, ENM for Membrane Proteins, Pemra Doruker
11:20-11:40	Break / Social
11:40-1:00	Allostery and Druggability Simulations, Burak Kaynak and Pemra Doruker
1:00-1:20	Q & A
1:20-2:00	Lunch/ Dinner Break
2:00-3:30	Evol and SignDy, Daniel Penaherrera and Bentley Wingert Membrane ANM, Daniel Penaherrera
3:30-3:50	Break / Social
3:50-5:45	ESSA, Burak Kaynak Druggability Suite, Jiyoung Lee
*Note that schedule is in Central Daylight time
Wednesday, June 30
*Molecular Visualization with VMD and MD Simulations with NAMD*
9:30-10:00	Breakfast / Social
10:00-11:20	Introduction to Biomolecular Simulation, Emad Tajkhorshid Molecular Modeling, Visualization, and Analysis in VMD, John Stone
11:20-11:40	Break / Social
11:40-1:00	Introduction to Molecular Dynamics Simulation, Emad Tajkhorshid NAMD Features and Capabilities, Mohammad S. Barhaghi Creating publication-quality images and (VR) movies with VMD, Barry Israelowitz
1:00-1:20	Q & A
1:20-2:00	Lunch Break / Social / Poster
2:00-3:30	Tutorial session I NAMD Tutorial VMD Tutorial
3:30-3:50	Break / Social
3:50-5:45	Tutorial session II NAMD Tutorial (cont.) VMD Tutorial (cont.)
*Note that schedule is in Central Daylight time
Thursday, July 1
*Introduction to Advanced Simulation Techniques, QwikMD, and Parameterization for Classical Force Fields with FFTK.*
9:00-10:00	Breakfast / Social
10:00-11:20	Introduction to Enhanced Sampling, Non-equilibrium & Free Energy Methods, Emad Tajkhorshid Overview of Free Energy Methods and Collective Variables in NAMD, Mohammad S. Barhaghi
11:20-11:40	Break / Social
11:40-1:00	QwikMD: Easy preparation of Molecular Dynamics Simulations, Rafael Bernardi FFTk: Parameterizing small molecules with Force-Field Toolkit, Mariano Spivak
1:00-1:20	Q & A
1:20-2:00	Lunch Break / Poster
2:00-3:30	Tutorial session I Free Energy Tutorial Colvar Tutorial QwikMD Tutorial
3:30-3:50	Break / Social
3:50-5:45	Tutorial session II Free Energy Tutorial Colvar Tutorial QwikMD Tutorial
*Note that schedule is in Central Daylight 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.