The workshop will present computational approaches for the simulation
of enzymatic reactions. Lectures will be held on the relevant
theoretical background including the applicability of Quantum Chemical
(QC) methods for large molecules, re-parameterization of Semiempirical
Molecular Orbital (SMO) methods for specific reactions, molecular
mechanics (MM) force fields, hybrid QC/MM potential energy functions
and simulation techniques on high performance computers. In-depth
tutorials will be presented primarily with the use of the freely
available pDynamo package developed in the lab of Dr. Martin J. Field
and will also include developing SMO parameters for quantitatively
accurate enzyme reaction simulations, the issues involved in
constructing a QC/MM model and the various methods for generating
energy profiles of bio-molecular reactions to determine mechanisms and
structure-function relationships. 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.
This workshop is funded by a grant from the NIH National Center for
Research Resources. These grants provide tuition and hotel costs,
supercomputing time, and workshop materials for US academic
All participants are responsible for paying their own travel expenses.
Complimentary continental breakfasts and lunches will be provided the
days of the workshop.