Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 10, Issue 7, Pages 2648-2657Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ct5002363
Keywords
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Funding
- National Institutes of Health (NIH) through the NIH Director's New Innovator Award Program [DP2-OD007237]
- National Institutes of Health (NIH) through NSF XSEDE Supercomputer resources grant [RAC CHE060073N]
- National Biomedical Computation Resource, NIH [P41 GM103426]
- National Center for Multiscale Modeling of Biological Systems (MM Bios) through from the National Institutes of Health [P41GM103712-S1]
- Office of Advanced Cyberinfrastructure (OAC)
- Direct For Computer & Info Scie & Enginr [0910735] Funding Source: National Science Foundation
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Owing to recent developments in computational algorithms and architectures, it is now computationally tractable to explore biologically relevant, equilibrium dynamics of realistically sized functional proteins using all-atom molecular dynamics simulations. Molecular dynamics simulations coupled with Markov state models is a nascent but rapidly growing technology that is enabling robust exploration of equilibrium dynamics. The objective of this work is to explore the challenges of coupling molecular dynamics simulations and Markov state models in the study of functional proteins. Using recent studies as a framework, we explore progress in sampling, model building, model selection, and coarse-grained analysis of models. Our goal is to highlight some of the current challenges in applying Markov state models to realistically sized proteins and spur discussion on advances in the field.
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