title: Computational models of protein kinematics and dynamics: beyond simulation.
abstract: Physics-based simulation represents a powerful method for investigating the time-varying behavior of dynamic protein systems at high spatial and temporal resolution. Such simulations, however, can be prohibitively difficult or lengthy for large proteins or when probing the lower-resolution, long-timescale behaviors of proteins generally. Importantly, not all questions about a protein system require full space and time resolution to produce an informative answer. For instance, by avoiding the simulation of uncorrelated, high-frequency atomic movements, a larger, domain-level picture of protein dynamics can be revealed. The purpose of this review is to highlight the growing body of complementary work that goes beyond simulation. In particular, this review focuses on methods that address kinematics and dynamics, as well as those that address larger organizational questions and can quickly yield useful information about the long-timescale behavior of a protein.
authors.affiliation: Computer Science Department, Rice University, Houston, Texas 77005, USA. bryant.gipson@rice.edu
authors.forename: Bryant
authors.initials: B
authors.lastname: Gipson
authors.forename: David
authors.initials: D
authors.lastname: Hsu
authors.forename: Lydia E
authors.initials: LE
authors.lastname: Kavraki
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: Latombe
mesh_terms: D000818:Animals; D001696:Biomechanical Phenomena; D003198:Computer Simulation; D006801:Humans; D008954:Models, Biological; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins