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

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  • 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

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Original languageEnglish
Pages (from-to)e1393
JournalWiley Interdisciplinary Reviews: Computational Molecular Science
Early online date27 Sep 2018
Publication statusE-pub ahead of print - 27 Sep 2018


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, e.g. 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 highlight examples of its application to investigate questions in biology.

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