title: Computing ensembles of transitions with molecular dynamics simulations.
abstract: A molecular understanding of conformational change is important for connecting structure and function. Without the ability to sample on the meaningful large-scale conformational changes, the ability to infer biological function and to understand the effect of mutations and changes in environment is not possible. Our Dynamic Importance Sampling method (DIMS), part of the CHARMM simulation package, is a method that enables sampling over ensembles of transition intermediates. This chapter outlines the context for the method and the usage within the program.
authors.affiliation: Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews, Room 3143, Urbana, IL, 61801, USA, juan@ks.uiuc.edu.
authors.forename: Juan R
authors.initials: JR
authors.lastname: Perilla
authors.forename: Thomas B
authors.initials: TB
authors.lastname: Woolf
mesh_terms: D000465:Algorithms; D006801:Humans; D056004:Molecular Dynamics Simulation; D025341:Principal Component Analysis; D055503:Protein Multimerization; D020893:Receptor, ErbB-3 / Q000737:chemistry
chemical_list: C581292:ERBB3 protein, human; D020893:Receptor, ErbB-3