The DOI matches its Crossref record; 137 of the 137 references it cites were found in a registry or an index.
Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions
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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“methods such as diffusion maps 9,77-79 try to link geometric data to the characteristic time scale of the system's motion.”
From Unsupervised machine learning in atomistic simulations, between predictions and understanding (2019) · cites this paper as [9]
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Allen, M. P., & Tildesley, D. J. (2017) · doi:10.1093/oso/9780198803195.001.0001 · Cited by 20,945
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Metadata
- Authors
- Rohrdanz, M. A., Zheng, W., & Clementi, C.
- Affiliations
- Rice University (US)
- 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
- 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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