Biomolecular simulation and modelling: status, progress and prospects
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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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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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Experimental — accuracy not yet measuredThe 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].”
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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- 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
- Publisher
- The Royal Society
- Published
- 2008-07-08
- Volume
- 5
- Issue
- suppl_3
- Pages
- 173-190
- ISSN
- 1742-5662 (ISSN-L)
- 1742-5689
- PMC
- PMC2706107
- 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
- green
- www.ncbi.nlm.nih.gov
- 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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