Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, the University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Chem Commun (Camb). 2014 Jan 11;50(3):262-82. doi: 10.1039/c3cc47148a. Epub 2013 Nov 20.
With computational resources becoming more efficient and more powerful and at the same time cheaper, computational methods have become more and more popular for studies on biochemical and biomimetic systems. Although large efforts from the scientific community have gone into exploring the possibilities of computational methods for studies on large biochemical systems, such studies are not without pitfalls and often cannot be routinely done but require expert execution. In this review we summarize and highlight advances in computational methodology and its application to enzymatic and biomimetic model complexes. In particular, we emphasize on topical and state-of-the-art methodologies that are able to either reproduce experimental findings, e.g., spectroscopic parameters and rate constants, accurately or make predictions of short-lived intermediates and fast reaction processes in nature. Moreover, we give examples of processes where certain computational methods dramatically fail.
随着计算资源变得更加高效、强大，同时也更加廉价，计算方法在生化和仿生系统的研究中变得越来越流行。尽管科学界已经做出了巨大的努力来探索计算方法在大型生化系统研究中的可能性，但这些研究并非没有陷阱，而且通常不能常规进行，而是需要专家来执行。在这篇综述中，我们总结并强调了计算方法及其在酶和仿生模型复合物中的应用方面的进展。特别是，我们强调了能够准确再现实验发现（例如光谱参数和速率常数）或对自然界中短寿命中间体和快速反应过程进行预测的热门和最先进的方法。此外，我们还给出了某些计算方法明显失败的例子。
