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Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions

Rohrdanz, Mary A., Zheng, Wenwei, Clementi, Cecilia·2013·Annual Review of Physical Chemistry

DOI 10.1146/annurev-physchem-040412-110006

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Abstract

The long-timescale dynamics of macromolecular systems can be oftentimes viewed as a reaction connecting metastable states of the system. In the past decade, various approaches have been developed to discover the collective motions associated with this dynamics. The corresponding collective variables are used in many applications, e.g., to understand the reaction mechanism, to quantify the system's free energy landscape, to enhance the sampling of the reaction path, and to determine the reaction rate. In this review we focus on a number of key developments in this field, providing an overview of several methods along with their relative regimes of applicability.

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See all 242

Authors: Rohrdanz, M. A., Zheng, W., & Clementi, C.
Affiliations: Rice University (US)
ORCID: Zheng, Wenwei
Clementi, Cecilia
Venue: Annual Review of Physical Chemistry
Publisher: Annual Reviews
Published: 2013-04-01
Volume: 64
Issue: 1
Pages: 295-316
ISSN: 0066-426X (ISSN-L)
1545-1593
DOI: 10.1146/annurev-physchem-040412-110006
OpenAlex: W2110497788
Cited by: 242
References: 137
Citations by year: 2026: 6 · 2025: 10 · 2024: 13 · 2023: 17 · 2022: 12 · 2021: 17 · 2020: 15 · 2019: 22 · 2018: 28 · 2017: 54 · 2016: 18 · 2015: 13 · 2014: 12 · 2013: 5
FWCI: 1.50
Type: journal article
Language: en
Open access: closed
Locations: Annual Review of Physical Chemistry (publishedVersion)
PubMed (publishedVersion)
Funders: National Science Foundation
Division of Chemistry
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Keywords: reaction coordinate, reaction pathways, collective variables, metastable states, free energy landscape, enhanced sampling, reaction mechanism, reaction rate, molecular dynamics

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Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions

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