Agenda

Monday, October 12:
Collective Dynamics of Proteins Using Elastic Network Models. From single molecules to biological assemblies

Time (CDT)*

Topic

Material

Video Lecture

09:30-10:00 Welcome and Brief Overview by Ivet Bahar Slides Recorded Session
10:00-11:20 Elastic Network Models (ENMs) and Collective Motions. Basic Theory and Methods, DynOmics Server, Ivet Bahar Slides Recorded Session
11:20-11:40 Break / Social    
11:40-13:00 Ensemble Analysis of Structures for Inferring Functional Mechanisms, ProDy and hybrid simulation methods, Pemra Doruker Slides Recorded Session
13:00-13:20 Q & A    
13:20-14:00 Lunch / Dinner break    
14:00-15:30 ProDy API Basics, Yan Zhang
GNM Analysis of Equilibrium Dynamics, Burak Kaynak
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Recorded Session
15:30-15:50 Break / Social    
15:50-17:45 ANM Analysis of Collective Motions and Visualization by NMWiz, Burak Kaynak
Ensemble Analysis by ProDy, Bentley Wingert
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Recorded Session

Tuesday, October 13:
Bridging Sequence, Structure and Function, and Experiments and Computations. Signature dynamics of families and Allosteric Signaling. Modeling and Simulations of Environmental Effects, Membrane Proteins and Druggability

Time (CDT)*

Topic

Material

Video Lecture

09:30-10:00 Social    
10:00-11:20 Evol: Bridging Sequence and Structure, Signature Dynamics of Protein Families, Perturbation Response Scanning, Allosteric Communication: Sensors and Effectors, Ivet Bahar Slides Recorded Session
11:20-11:40 Break / Social    
11:40-13:00 ENM for Membrane Proteins using Environment Approach for Lipid Bilayer,
Druggability Simulations, Pemra Doruker
Slides Recorded Session
13:00-13:20 Q & A    
13:20-14:00 Lunch / Dinner break    
14:00-15:30 Evol and SignDy, James Krieger
PRS, James Krieger
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Recorded Session
15:30-15:50 Break / Social    
15:50-17:45 Membrane proteins and environmental effects, Yan Zhang
Druggability Suite, Jiyoung Lee
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Recorded Session

Wednesday, October 14:
Molecular Visualization with VMD and MD Simulations with NAMD

Time (CDT)*

Topic

Material

Video Lecture

09:30-10:00 Social    
10:00-11:20 Introduction to Biomolecular Simulation, Emad Tajkhorshid
Molecular Modeling, Visualization, and Analysis in VMD, John Stone
 Slides  Recorded Session
11:20-11:40 Break / Social    
11:40-13:00 NAMD Features and Capabilities, David Hardy
Performance and GPU Acceleration in NAMD, Julio Maia
 Slides  Recorded Session
13:00-13:20 Q & A    
13:20-14:00 Lunch / Dinner break    
14:00-15:30 Tutorial session I
NAMD Tutorial
VMD Tutorial
 Tutorials  No recording
15:30-15:50 Break / Social    
15:50-17:45 Tutorial session II
NAMD Tutorial (cont.)
VMD Tutorial (cont.)
 Tutorials  No recording

Thursday, October 15:
Introduction to Advanced Simulation Techniques, QwikMD, and Parameterization for Classical Force Fields with FFTK

Time (CDT)*

Topic

Material

Video Lecture

09:30-10:00 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
 Slides Recorded Session
11:20-11:40 Break / Social    
11:40-13:00 QwikMD: Easy preparation of Molecular Dynamics Simulations, Rafael Bernardi
ffTk: Parameterizing small molecules with Force-Field Toolkit, Mariano Spivak
 Slides Recorded Session
13:00-13:20 Q & A    
13:20-14:00 Lunch / Dinner break    
14:00-15:30 Tutorial session I
Free Energy Tutorial
Colvar Tutorial
QwikMD Tutorial
 Tutorials Recorded Session
15:30-15:50 Break / Social    
15:50-17:45 Tutorial session II
Free Energy Tutorial
Colvar Tutorial
QwikMD Tutorial
 Tutorials Recorded Session