Computational Biophysics Workshop - San Francisco, December 12-16, 2016

Program

Location: QB3 Byers Hall 215

Monday, December 12: Principles and Applications of Molecular Dynamics Simulations with NAMD

08:00-09:30          Introduction to Molecular Dynamics with NAMD I (Rafael Bernardi)
09:30-09:50          Coffee Break
09:50-11:20          Introduction to Molecular Dynamics with NAMD II (Rafael Bernardi)
11:20-11:40          Q & A
11:40-13:00          Lunch Break
13:00-14:50          Tutorials
14:50-15:10          Coffee Break
15:10-17:00          Tutorials

Tuesday, December 13: Molecular Simulation, Analysis, and Visualization with QwikMD and VMD

08:00-09:30          Integrative Modeling I and QwikMD Demo (Till Rudack)
09:30-09:50          Coffee Break
09:50-11:20          Visualization and Image Making with VMD and Capabilities Demo (Jodi Hadden)
11:20-11:40          Q & A
11:40-13:00          Lunch Break
13:00-14:50          Tutorials
14:50-15:10          Coffee Break
15:10-17:00          Tutorials

Wednesday, December 14: Principles and Applications of Molecular Dynamics Flexible Fitting

08:00-09:30          Introduction to MDFF (Ryan McGreevy)
09:30-09:50          Coffee Break
09:50-11:20          Integrative Modeling II (Till Rudack)
11:20-11:40          Q & A
11:40-13:00          Lunch Break
13:00-14:50          Tutorials
14:50-15:10          Coffee Break
15:10-17:00          Tutorials

Thursday, December 15: Integrative Modeling Platform I

08:00-09:30          Introduction to Integrative Modeling and IMP (Andrej Sali)
09:30-09:50          Coffee Break
09:50-11:20          Modeling of the Nup84 Subcomplex of the NPC (Ben Webb and Seung Joong Kim)
11:20-11:40          Q & A
11:40-13:00          Lunch Break
13:00-14:50          Guided Tutorial: IMP installation, setup, and basic modeling (Ben Webb)
14:50-15:10          Coffee Break
15:10-17:00          IMP analysis (Ben Webb)

IMP Lectures

Friday, December 16: Integrative Modeling Platform II

08:00-09:30          Guided Tutorial: Application of IMP to a complex system, Nup82: part I (Seung Joong Kim, Ilan Chemmama)
09:30-09:50          Coffee Break
09:50-11:20          Guided Tutorial: Application of IMP to a complex system, Nup82: part II (Seung Joong Kim, Ilan Chemmama)
11:20-11:40          Q & A
11:40-13:00          Lunch Break
13:00-14:50          Guided Tutorial: Using a novel experimental data source with IMP (Seth Axen, Barak Raveh)
14:50-15:10          Coffee Break
15:10-17:00          Guided Tutorial: Validation of integrative models (Daniel Saltzberg)

IMP Lectures