Binding Energy Distribution Analysis Method (BEDAM): Hamiltonian replica exchange with torsional flattening for binding mode prediction and binding free energy estimation

Molecular dynamics modeling of complex biological systems is limited by finite simulation time. The simulations are often trapped close to local energy minima separated by high energy barriers. Here, we introduce Hamiltonian replica exchange (H-REMD) with torsional flattening in the Binding Energy D...

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Bibliographic Details
Published in:J Chem Theory Comput
Main Authors: Mentes, Ahmet, Deng, Nan-Jie, Vijayan, R. S. K., Xia, Junchao, Gallicchio, Emilio, Levy, Ronald M.
Format: Artigo
Language:Inglês
Published: 2016
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Article
Online Access:https://ncbi.nlm.nih.gov/pmc/articles/PMC4862910/
https://ncbi.nlm.nih.gov/pubmed/27070865
https://ncbi.nlm.nih.govhttp://dx.doi.org/10.1021/acs.jctc.6b00134
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