Computational Biophysics Workshop - Urbana, Nov. 18-22, 2013
Program
- Lectures: Room 3269 of the Beckman Institute
- Tutorials: Room 3269 and TCBG Innovation Areas I & II at Beckman
Mon, Nov 18: Introduction to Protein Structure and Dynamics - Klaus Schulten
| 08:30-09:00 | Registration and continental breakfast |
| 09:00-09:10 | Opening Remarks |
| 09:10-10:40 | Structure and Sequence Analysis with VMD |
| Coffee Break | |
| 11:00-12:00 | Introduction to Molecular Dynamics with NAMD |
| 12:00-12:20 | Q & A |
| Lunch Break | |
| 13:30-14:00 | NAMD from the Developer's Perspective - Jim Phillips |
| 14:00-16:00 | VMD Tutorial - Using VMD; NAMD Tutorial |
| Coffee Break | |
| 16:15-18:00 | VMD Tutorial - Using VMD; NAMD Tutorial |
Tue, Nov 19: Force Field Parameterization - Emad Tajkhorshid
| 08:30-09:00 | Continental breakfast |
| 09:00-10:30 | Introduction to Topology, Parameters, and Structure Files |
| Coffee Break | |
| 10:50-12:00 | Topology, Parameters, and Structure Files |
| 12:00-12:20 | Q & A |
| Lunch Break | |
| 13:30-14:00 | Force Field Toolkit (ffTK) - Chris Mayne |
| 14:00-16:00 | Parameterizing a Novel Residue; Topology File Tutorial |
| Coffee Break | |
| 16:15-18:00 | Parameterizing a Novel Residue; Topology File Tutorial - Participant tutorial options: NAMD Tutorial & Stretching Deca-alanine |
Wed, Nov 20: Computational Nano-Bio - Alek Aksimentiev
| 08:30-09:00 | Continental breakfast |
| 09:00-10:30 | Introduction to Modeling and Simulations of Nucleic Acid Systems |
| Coffee Break | |
| 10:50-12:00 | Modeling the Interface Between Biological and Synthetic Materials |
| 12:00-12:20 | Q & A |
| Lunch Break | |
| 14:00-16:30 | Modeling Nanopores for Sequencing DNA; Visualizing MD Results: Stretching dsDNA Mini Tutorial; Introduction to MD Simulation of DNA-protein Systems; User-Defined Forces in NAMD |
| Coffee Break | |
| 16:45-18:00 | Modeling Nanopores for Sequencing DNA; Visualizing MD Results: Stretching dsDNA Mini Tutorial; Introduction to MD Simulation of DNA-protein Systems; User-Defined Forces in NAMD |
Thu, Nov 21: Introduction to Bioinformatics - Zaida Luthey-Schulten
| 08:30-09:00 | Continental breakfast |
| 09:00-10:30 | Part I - Introduction to Evolutionary Concepts and VMD/MultiSeq Part II - Applications of MultiSeq Evolution of Translation: Dynamics of Recognition in RNA:Protein Complexes |
| Coffee Break | |
| 10:50-12:00 | Part III - Towards in silico Cells: Simulating Processes in Entire Cells |
| 12:00-12:30 | Q & A; Group picture |
| Lunch Break | |
| 13:30-14:00 | VMD from the Developer's Perspective - Kirby Vandivort |
| 14:00-16:00 | Basic Sequence Analysis: Aquaporins with the VMD MultiSeq
Tool; or |
| Coffee Break | |
| 16:15-18:00 | Basic Sequence Analysis: Aquaporins with the VMD MultiSeq
Tool; or Expert Sequence Analysis - Evolution of Translation Class I Aminoacyl-tRNA Synthetases: tRNA complexes - Evolution of Translation EF-Tu: tRNA - Evolution of Translation: The Ribosome; or, Dynamical Network Analysis, or Participants work on their own projects |
Fri, Nov 22: Simulating Membrane Proteins - Emad Tajkhorshid
| 08:30-09:00 | Continental breakfast |
| 09:00-10:30 | Introduction and Examples |
| Coffee Break | |
| 10:50-12:00 | Transport in Membrane Channels |
| 12:00-12:20 | Q & A |
| Lunch Break | |
| 13:30-14:00 | Molecular Dynamics Flexible Fitting - Ryan McGreevy |
| 14:00-16:30 | Membrane Proteins Tutorial; Open tutorial time |
| Coffee Break | |
| 16:45-18:00 | Membrane Proteins Tutorial; Open tutorial 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".
