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Development and application of enhanced sampling techniques to simulate the long‐time scale dynamics of biomolecular systems
Author(s) -
Spiriti Justin,
Kamberaj Hiqmet,
Van Der Vaart Arjan
Publication year - 2012
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.23139
Subject(s) - molecular dynamics , sampling (signal processing) , dynamics (music) , isomerization , scale (ratio) , computer science , quantum , statistical physics , chemistry , nanotechnology , computational chemistry , physics , materials science , quantum mechanics , biochemistry , filter (signal processing) , acoustics , computer vision , catalysis
The behavior of proteins and DNA is largely determined by their dynamics, which involves transitions between various conformational states. Computer simulations can provide detailed insights into these dynamics, but the long‐time scales of the transitions severely complicate such an approach. In this review, we present a few recently developed enhanced sampling techniques for the simulation of conformational changes at atomic resolution. To illustrate the application of these techniques, we discuss the isomerization of a nonprolyl peptide bond in a collagenase and a joint simulation‐experimental study of a DNA‐dye system. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2012