Abstract:
As the database of solved protein tertiary structures continues to grow the scientific community will be able to understand more and more fundamental connections between protein structure and its measured function. A critical part of the mapping from the structure to the function will be to get an improved understanding of the conformational motions present in each protein. A subset of these proteins have been determined in two or more conformations. This sets up the problem of understanding transitions between defined states. Our method, dynamic importance sampling (DIMS), is designed to efficiently sample on transition pathways between two defined states. In principle this allows us to compute kinetics, relative free energies and multiple pathways between two conformations. The talk will focus on the dynamic importance sampling algorithm and its application to several systems. The current version of DIMS is available in CHARMM.