Computational Biophysics Workshop - June 28 - July 1, 2021
Agenda
Monday, June 28:
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, Ivet Bahar | Slides | Recorded Session |
| 11:20-11:40 | Break / Social | ||
| 11:40-13:00 | Bridging structure and function, theory and experiments Ivet Bahar Ensemble Analysis of Structures for Inferring Functional Mechanisms, DynOmics Server, 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, Burak Kaynak GNM Analysis of Equilibrium Dynamics, Burak Kaynak |
jupyter_nb jupyter_nb |
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 |
jupyter_nb jupyter_nb data file |
Recorded Session |
Tuesday, June 29:
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
|
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 |
jupyter_nb jupyter_nb |
Recorded Session |
| 15:30-15:50 | Break / Social | ||
| 15:50-17:45 | Membrane proteins and environmental effects, Yan Zhang Druggability Suite, Jiyoung Lee |
jupyter_nb files data files |
Recorded Session |
Wednesday, June 30:
Molecular Simulation and Visualization with NAMD and VMD
|
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 |
SlidesSlides | Recorded Session |
| 11:20-11:40 | Break / Social | ||
| 11:40-13:00 | NAMD Features and Capabilities, Mohammad S. Barhaghi Modeling and Parametrization of Small Molecules with Molefacture and Force-Field Toolkit, Mariano Spivak |
SlidesSlides | Recorded Session |
| 13:00-13:20 | Q & A | ||
| 13:20-14:00 | Lunch 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, July 1:
Introduction to Advanced Simulation Techniques and QwikMD
|
Time (CDT)* |
Topic |
Material |
Video Lecture |
| 09:30-10:00 | Social | ||
| 10:00-11:20 | Battling the Timescale in Classical MD Simulations - Introduction to Enhanced Sampling and Non-equilibrium methods, Emad Tajkhorshid | Slides | Recorded Session |
| 11:20-11:40 | Break / Social | ||
| 11:40-13:00 | QwikMD: Easy preparation of Molecular Dynamics Simulations, Rafael Bernardi Creating Publication-quality Images and Movies with VMD, Rafael Bernardi, Rafael Bernardi |
Slides | Recorded Session |
| 13:00-13:20 | Q & A | ||
| 13:20-14:00 | Lunch 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 |