Molecular dynamics simulations of large macromolecular complexes
JR Perilla and BC Goh and CK Cassidy and B Liu and RC Bernardi and T Rudack and H Yu and Z Wu and K Schulten, CURRENT OPINION IN STRUCTURAL BIOLOGY, 31, 64-74 (2015).
Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone.
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