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Computing Reaction Pathways of Rare Biomolecular Transitions using Atomistic Force-Fields
1Dipartimento di Fisica, Università degli Studi di Trento, Via Sommarive 14 Povo, Trento, 38123 Italy; Trento Institute for Fundamental Physics and Applications (INFN-TIFPA), Via Sommarive 14 Povo, Trento, 38123 Italy.
Abstract:
The Dominant Reaction Pathway (DRP) method is an approximate variational scheme which can be used to compute reaction pathways in conformational transitions undergone by large biomolecules (up to ~10(3) amino-acids) using realistic all-atom force fields. We first review the status of development of this method. Next, we discuss its validation against the results of plain MD protein folding simulations performed by the DE-Shaw group using the Anton supercomputer. Finally, we review a few representative applications of the DRP approach to study reactions which are far too complex and rare to be investigated by plain MD, even on the Anton machine.
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