Evidence map›Paper›PMID 27498634›Full record

ReviewMethods in enzymology2016

Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways.

D Wu, M I Fajer, L Cao, X Cheng, W Yang

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Methods in enzymology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
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0citing papers in PubMed
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1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

D WuInstitute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States.
M I FajerUT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, United States; Florida State University, Tallahassee, FL, United States.
L CaoFlorida State University, Tallahassee, FL, United States.
X ChengUT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, United States; The University of Tennessee, Knoxville, TN, United States. Electronic address: chengx@ornl.gov.
W YangInstitute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States; Florida State University, Tallahassee, FL, United States. Electronic address: yyang2@fsu.edu.

Funding

INOSINE MONOPHOSPHATE DEHYDROGENASER01GM054403 · NIGMS · BRANDEIS UNIVERSITY · PI HEDSTROM, LIZBETH K. · 1998 to 2016
$4.2M
Understanding Protein-Ligand RecogntionR01GM111886 · NIGMS · FLORIDA STATE UNIVERSITY · PI YANG, WEI · 2014 to 2018
$1.5M
NIGMS NIH HHS R01 GM054403NIGMS NIH HHS R01 GM111886
6 · The paper itself

Abstract

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.

Indexed as

AlgorithmsMolecular Dynamics SimulationThermodynamicsAnimalsEnzymesHumansEnzymesEnzyme reactionGeneralized ensemble samplingMinimum free energy path

Identifiers

PMID27498634
PMCPMC4978182

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.