Computer Simulation of Biomolecular Dynamics and Reactions

Workshop Dates: Tuesday, June 5 - Friday, June 8, 2012
Location: Pittsburgh Supercomputing Center, 300 South Craig Street, Pittsburgh, PA 15213
Registration Deadline: May 8, 2012
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PDF: Further information and Tentative Agenda

The workshop will present computational approaches for the simulation of biomolecular dynamics and reactions, primarily focusing on the latter. Lectures will be held on the relevant theoretical background including the prediction and analysis of protein dynamics using normal mode analyses (NMA) and elastic network models (ENM), molecular mechanics (MM) force field parameterization of small molecules, the applicability of Quantum Chemical (QC) methods for large molecules, re-parameterization strategies for improving Semiempirical Molecular Orbital (SMO) methods for specific reactions, and hybrid QC/MM potential energy functions and simulation techniques on high performance computers. In-depth tutorials will be presented on applying and interpreting the results from ENM-based NMA using ProDy developed in Prof. Ivet Bahar’s lab, MM force field parameterization of small molcules using a newly developed toolkit ParamIT, developing corrections to SMO methods for use in quantitatively-accurate free energy simulations, constructing a QC/MM model, and the various methods for generating energy profiles of bio-molecular reactions to determine mechanisms and structure-function relationships employing the freely available pDynamo package developed in the lab of Dr. Martin J. Field. Graphical user interfaces in Pymol and VMD for QC/MM model construction will also be demonstrated. Experience with pDynamo is helpful but not a prerequisite for attendance.

The workshop is designed for graduate students, post-doctoral researchers and faculty in computational biophysics and physical organic chemistry who have experience with computational chemistry methods and seek to enhance their capabilities to include the modeling of enzymatic reactions. Participants are encouraged to discuss and work on bio-molecular systems from their own research during the workshop. Space is limited.

Instructors include:

  • Martin J. Field (Institute of Structural Biology, Grenoble, France)
  • Timothy Lezon (University of Pittsburgh Medical School, Department of Computational Biology)
  • Ahmet Bakan (University of Pittsburgh Medical School, Department of Computational Biology)
  • Nikolay Simakov (Pittsburgh Supercomputing Center/NRBSC)
  • Jose Fernando Bachega (University of Sao Paulo)
  • Troy Wymore (Pittsburgh Supercomputing Center/NRBSC)

Registration will be free of charge for attendees from non-profit academic institutions. Participants are expected to cover their own travel and housing expenses.

If you have any questions, please contact Pat Sudac sudac@psc.edu.

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