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Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs

机译:酶过程的量子力学/分子力学建模:警告和突破

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摘要

Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black-box method that is easily applied, but requires careful set-up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work-protocols developed in our groups for running successful QM/MM calculations.
机译:大自然开发了大批酶催化剂,目的是将底物转移到有用的产品中,这使生物系统能够执行其所有自然功能。这样,我们体内的所有生化过程(我们喝酒,吃饭,呼吸,睡觉等)都受酶的控制。与生物催化剂研究相关的问题之一是它们的反应速度如此之快,以至于无法通过实验工作获得其反应机理的详细信息。近年来,计算硬件和软件取得了重大进步,现在可以使用精确的计算技术研究大型(生物)化学系统。一种这样的技术是量子力学/分子力学(QM / MM)技术,近年来已经获得了很大的发展。不幸的是,它不是容易应用的黑盒方法,而是需要仔细的设置过程。在这项工作中,我们对QM / MM的技术难题和警告进行了概述,并讨论了我们小组为成功运行QM / MM计算而开发的工作协议。

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