Cited by 410Protein Structure and DynamicsRNA and protein synthesis mechanismsAdvanced Physical and Chemical Molecular Interactions

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To milliseconds and beyond: challenges in the simulation of protein folding

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Lane, Thomas J, Shukla, Diwakar, Beauchamp, Kyle A, Pande, Vijay S·2013·Current Opinion in Structural Biology

DOI 10.1016/j.sbi.2012.11.002PMC PMC3673555

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Abstract

Quantitatively accurate all-atom molecular dynamics (MD) simulations of protein folding have long been considered a holy grail of computational biology. Due to the large system sizes and long timescales involved, such a pursuit was for many years computationally intractable. Further, sufficiently accurate forcefields needed to be developed in order to realistically model folding. This decade, however, saw the first reports of folding simulations describing kinetics on the order of milliseconds, placing many proteins firmly within reach of these methods. Progress in sampling and forcefield accuracy, however, presents a new challenge: how to turn huge MD datasets into scientific understanding. Here, we review recent progress in MD simulation techniques and show how the vast datasets generated by such techniques present new challenges for analysis. We critically discuss the state of the art, including reaction coordinate and Markov state model (MSM) methods, and provide a perspective for the future.

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Authors: Lane, T. J., Shukla, D., Beauchamp, K. A., & Pande, V. S.
Affiliations: Stanford University (US)
Corresponding author: Pande, Vijay S
ORCID: Lane, Thomas J
Shukla, Diwakar
Beauchamp, Kyle A
Pande, Vijay S
Venue: Current Opinion in Structural Biology
Publisher: Elsevier BV
Published: 2013-02
Volume: 23
Issue: 1
Pages: 58-65
ISSN: 0959-440X (ISSN-L)
DOI: 10.1016/j.sbi.2012.11.002
PMC: PMC3673555
OpenAlex: W2039369142
Cited by: 409
References: 92
Citations by year: 2026: 13 · 2025: 21 · 2024: 11 · 2023: 22 · 2022: 21 · 2021: 23 · 2020: 26 · 2019: 26 · 2018: 38 · 2017: 70 · 2016: 38 · 2015: 44 · 2014: 36 · 2013: 20
FWCI: 2.92
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Current Opinion in Structural Biology (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
Funders: Simbios NIH Center for Biomedical Computation (GM072970)
NIH (R01GM62828)
NSF GRF
Stanford Graduate Fellowship
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
Keywords: protein folding, all-atom molecular dynamics, folding kinetics, force fields, reaction coordinate, Markov state models, sampling efficiency
MeSH terms: Kinetics, Proteins, Protein Folding, Molecular Dynamics Simulation

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To milliseconds and beyond: challenges in the simulation of protein folding

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