Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity
Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity
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DOI：
10.1002/wcms.1393
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发表时间：
2019-05-01
影响因子：
11.4
通讯作者：
van der Kamp, Marc W.
中科院分区：
文献类型：
--
作者：
Huggins, David J.;Biggin, Philip C.;van der Kamp, Marc W.
生物分子模拟对于理解和设计生物分子及其相互作用越来越重要。详细的，基于物理学的模拟方法在生物催化，药物输送，生物材料，生物技术和药物设计等领域的影响正在迅速增长。模拟提供了对机制、动力学和过程的独特详细的原子级洞察的潜力，以及对分子性质的日益准确的预测。模拟现在可以用作生物活性的计算分析，例如，在预测耐药性中。方法和算法的发展，加上计算硬件的进步，正在改变计算的范围和范围。不同类型的问题需要不同类型的方法。准确的方法和广泛的模拟承诺与整个生物化学实验的定量比较。原子模拟现在可以访问大型系统的实验相关的时间尺度，导致实验和理论的丰富的相互作用，并为验证和开发模型提供前所未有的机会。粗粒度的方法允许更大的长度和时间尺度的研究，和理论的发展带来的电子结构计算到新的制度。多尺度方法是开发的另一个关键焦点，结合不同层次的理论以提高准确性，旨在将化学和分子变化与宏观观测值联系起来。在这篇综述中，我们概述了生物分子模拟方法，并强调其应用的例子，以调查生物学中的问题。本文分类下：分子和统计力学>分子动力学和蒙特-卡罗方法结构和机制>计算生物化学和生物物理分子和统计力学>自由能方法
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