Cited by 90Protein Structure and DynamicsAdvanced Physical and Chemical Molecular InteractionsComputational Drug Discovery Methods

Biomolecular simulation and modelling: status, progress and prospects

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van der Kamp, Marc W, Shaw, Katherine E, Woods, Christopher J, Mulholland, Adrian J·2008·Journal of The Royal Society Interface

Abstract

Molecular simulation is increasingly demonstrating its practical value in the investigation of biological systems. Computational modelling of biomolecular systems is an exciting and rapidly developing area, which is expanding significantly in scope. A range of simulation methods has been developed that can be applied to study a wide variety of problems in structural biology and at the interfaces between physics, chemistry and biology. Here, we give an overview of methods and some recent developments in atomistic biomolecular simulation. Some recent applications and theoretical developments are highlighted.

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Crossref · 10.1098/rsif.2008.0105.focus

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  • Simulation might provide deeper insight into biological macromolecules, such as the association of small molecules with macromolecules, computation of ligand binding free energies, dynamics of transport and ion channels across membranes, and information that might be the basis of clinical features.

    “The simulation might provide a deeper insight into biological macromolecules, such as the association of small molecules with macromolecules, computation of ligand's binding free energies, dynamics of transport and ion channels across membranes, and the information might be the basis of clinical features.”

    From Quantum Computing in the Next-Generation Computational Biology Landscape: From Protein Folding to Molecular Dynamics (2024) · cites this paper as [62]

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  • The study might contribute to the structure and function relationship of biological macromolecules.

    “The study might contribute to the structure and function relationship of biological macromolecules [62].”

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1 of the 239 references couldn’t be matched to a known paper.

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  1. Roitberg, A. E. 2005 Non-equilibrium approaches to free energy calculations. In Annual reports in computational chemistry, vol. 1 (ed. C. Simmerling), pp. 103–112. Oxford, UK: Elsevier.

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Authors
van der Kamp, M. W., Shaw, K. E., Woods, C. J., & Mulholland, A. J.
Affiliations
  • Centre for Computational Chemistry, School of Chemistry, University of BristolBristol BS8 1TS, UK
  • University of Bristol (GB)
Venue
Journal of The Royal Society Interface
Published
2008-07-08
Volume
5
Issue
suppl_3
Pages
173-190
ISSN
  • 1742-5662 (ISSN-L)
  • 1742-5689
OpenAlex
W2128116330
Cited by
90
References
239
Citations by year
2025: 1 · 2024: 6 · 2023: 4 · 2022: 5 · 2021: 1 · 2020: 1 · 2019: 5 · 2018: 6 · 2017: 2 · 2016: 2 · 2015: 4 · 2014: 6 · 2013: 7 · 2012: 12
FWCI
0.72
Type
journal article
Language
en
Open access
Locations
  • Journal of The Royal Society Interface (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • Explore Bristol Research (publishedVersion)
  • Bristol Research (University of Bristol) (submittedVersion)
Funders
  • Engineering and Physical Sciences Research Council (EP/E022197/1, EP/F010516/1, GR/R86119/01, EP/G007705/1)
  • Biotechnology and Biological Sciences Research Council (BB/D52212X/1)
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
  • Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
Keywords
biomolecular simulation, atomistic simulation, structural biology, simulation methods, multiscale modeling
MeSH terms
Computer Simulation, Enzymes, Models, Molecular, Molecular Biology, Quantum Theory, Computational Biology

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