Biomolecular simulations: from dynamics and mechanisms to computational assays of biological activity

David J. Huggins*, Philip C. Biggin, Marc A. Dämgen, Jonathan W. Essex, Sarah A. Harris, Richard H. Henchman, Syma Khalid, Antonija Kuzmanic, Charles A. Laughton, Julien Michel, Adrian J. Mulholland, Edina Rosta, Mark S.P. Sansom, Marc W. van der Kamp

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

42 Citations (Scopus)
259 Downloads (Pure)

Abstract

Biomolecular simulation is increasingly central to understanding and designing biological molecules and their interactions. Detailed, physics-based simulation methods are demonstrating rapidly growing impact in areas as diverse as biocatalysis, drug delivery, biomaterials, biotechnology, and drug design. Simulations offer the potential of uniquely detailed, atomic-level insight into mechanisms, dynamics, and processes, as well as increasingly accurate predictions of molecular properties. Simulations can now be used as computational assays of biological activity, for example, in predictions of drug resistance. Methodological and algorithmic developments, combined with advances in computational hardware, are transforming the scope and range of calculations. Different types of methods are required for different types of problem. Accurate methods and extensive simulations promise quantitative comparison with experiments across biochemistry. Atomistic simulations can now access experimentally relevant timescales for large systems, leading to a fertile interplay of experiment and theory and offering unprecedented opportunities for validating and developing models. Coarse-grained methods allow studies on larger length- and timescales, and theoretical developments are bringing electronic structure calculations into new regimes. Multiscale methods are another key focus for development, combining different levels of theory to increase accuracy, aiming to connect chemical and molecular changes to macroscopic observables. In this review, we outline biomolecular simulation methods and highlight examples of its application to investigate questions in biology. This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Free Energy Methods.

Original languageEnglish
Article numbere1393
Number of pages23
JournalWiley Interdisciplinary Reviews: Computational Molecular Science
Early online date27 Sep 2018
DOIs
Publication statusE-pub ahead of print - 27 Sep 2018

Structured keywords

  • BrisSynBio
  • Bristol BioDesign Institute

Keywords

  • enzyme
  • membrane
  • molecular dynamics
  • multiscale
  • protein
  • QM/MM
  • Synthetic Biology

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