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Title: Computational models of protein kinematics and dynamics: Beyond simulation
Authors: Gipson, B.
Hsu, D. 
Kavraki, L.E.
Latombe, J.-C.
Keywords: conformation sampling
geometric methods
graph-based methods
kinematic models
protein motion
Issue Date: 2012
Citation: Gipson, B., Hsu, D., Kavraki, L.E., Latombe, J.-C. (2012). Computational models of protein kinematics and dynamics: Beyond simulation. Annual Review of Analytical Chemistry 5 : 273-291. ScholarBank@NUS Repository.
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. Copyright © 2012 by Annual Reviews. All rights reserved.
Source Title: Annual Review of Analytical Chemistry
ISSN: 19361327
DOI: 10.1146/annurev-anchem-062011-143024
Appears in Collections:Staff Publications

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