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Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways.

Title: Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways.
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Name(s): Wu, D, author
Fajer, M I, author
Cao, L, author
Cheng, X, author
Yang, W, author
Type of Resource: text
Genre: Journal Article
Text
Date Issued: 2016-01-01
Physical Form: computer
online resource
Extent: 1 online resource
Language(s): English
Abstract/Description: Free energy path sampling plays an essential role in computational understanding of chemical reactions, particularly those occurring in enzymatic environments. Among a variety of molecular dynamics simulation approaches, the generalized ensemble sampling strategy is uniquely attractive for the fact that it not only can enhance the sampling of rare chemical events but also can naturally ensure consistent exploration of environmental degrees of freedom. In this review, we plan to provide a tutorial-like tour on an emerging topic: generalized ensemble sampling of enzyme reaction free energy path. The discussion is largely focused on our own studies, particularly ones based on the metadynamics free energy sampling method and the on-the-path random walk path sampling method. We hope that this minipresentation will provide interested practitioners some meaningful guidance for future algorithm formulation and application study.
Identifier: FSU_pmch_27498634 (IID), 10.1016/bs.mie.2016.05.012 (DOI), PMC4978182 (PMCID), 27498634 (RID), 27498634 (EID), S0076-6879(16)30047-7 (PII)
Keywords: Enzyme reaction, Generalized ensemble sampling, Minimum free energy path
Grant Number: R01 GM054403, R01 GM111886
Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978182.
Subject(s): Algorithms
Animals
Enzymes/chemistry
Enzymes/metabolism
Humans
Molecular Dynamics Simulation
Thermodynamics
Persistent Link to This Record: http://purl.flvc.org/fsu/fd/FSU_pmch_27498634
Owner Institution: FSU
Is Part Of: Methods in enzymology.
1557-7988
Issue: vol. 577

Choose the citation style.
Wu, D., Fajer, M. I., Cao, L., Cheng, X., & Yang, W. (2016). Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways. Methods In Enzymology. Retrieved from http://purl.flvc.org/fsu/fd/FSU_pmch_27498634