Cryo-EM Modeling Based on X-ray Crystallography Workshop, Urbana, Jan. 8-10, 2014

Program

Locations:
  • Lectures: Room 3269 of the Beckman Institute
  • Tutorials: Room 3269 and TCBG Innovation Areas I & II at Beckman

Wed, Jan 8: Principles and Applications of Molecular Dynamics Flexible Fitting - Klaus Schulten and TCBG Members

08:30-09:00 Registration and Continental Breakfast
09:00-09:05 Opening Remarks
09:05-09:45 The Computational Microscope with VMD and NAMD
09:45-10:15 Principles of MDFF - Ryan McGreevy (pdf)
10:15-10:45 Applications of MDFF - Yan Chan and Juan Perilla (pdf, pdf)
Coffee Break and Group Photo
11:00-12:00 Demonstrations of MDFF* - Yan Chan, Boon Chong Goh, Yanxin Liu, Juan Perilla, Abhi Singaroy
12:00-12:20 Q & A
Lunch Break  
14:00-16:00 VMD Tutorial - Using VMD; NAMD Tutorial (possibly also MDFF, Structure Check tutorials)
Coffee Break  
16:15-18:00 VMD Tutorial - Using VMD; NAMD Tutorial (possibly also MDFF, Structure Check tutorials)
Dinner  

* Note: demonstrations will be shown in TCBG Innovation Courtyard II, across from Room 3055

Thu, Jan 9: Structural Modeling Using DireX and DEN - Gunnar Schroeder

08:30-09:00 Continental Breakfast
09:00-10:30 Fitting Cryo-EM Density Maps with Crystal Structures Using DireX (pdf)
Coffee Break  
10:50-12:00 Deformable Elastic Network (DEN) (pdf)
12:00-12:30 Q & A
Lunch Break  
14:00-16:00 DireX Tutorial (pdf); MDFF Tutorial; Structure Check Tutorial
Coffee Break  
16:15-18:00 DireX Tutorial (pdf); MDFF Tutorial; Structure Check Tutorial

 

Fri, Jan 10: Participant Projects, Tutorials, and Lab Time

08:30-09:00 Continental Breakfast
09:00-10:30 Participant Projects, Tutorials, and Lab Time
Coffee Break  
10:50-12:00 Participant Projects, Tutorials, and Lab Time
Lunch Break  
14:00-16:30

Participant Projects, Tutorials, and Lab Time
Coffee Break  
16:45-18:00 Participant Projects, Tutorials, and Lab Time

Click here to see descriptions of tutorials listed in program.

Note: program subject to change. Workshop supported by NIH 9P41GM104601 "Center for Macromolecular Modeling and Bioinformatics".