Abstract：
Elucidating the structure of an enzyme and how substrates bind to the active site is an important step for understanding its reaction mechanism and function. Nevertheless, the methods available to obtain three-dimensional structures of proteins, such as x-ray crystallography and NMR, can be expensive and time-consuming. Considering this, an alternative is using structural bioinformatic tools to predict the tertiary structure of a protein from its primary sequence, followed by molecular docking of one or more substrates into the enzyme structure model. In the past few years, significant advances have been made in these computational tools, which can give useful information about the active site and enzyme-substrate interactions before the structure can be resolved using physical methods. Here, using common bean (Phaseolus vulgaris) hydroxycinnamoyl-coenzyme A:tetrahydroxyhexanedioic acid hydroxycinnamoyltransferase (HHHT) as an example, we describe methods and workflows for protein structure prediction and molecular docking that can be performed on a personal computer using only open-source tools.
摘要：
阐明酶的结构以及底物如何与活性位点结合是了解其反应机理和功能的重要步骤。然而，获得蛋白质三维结构的方法，如X射线晶体学和核磁共振，可能是昂贵和耗时的。考虑到这一点,另一种选择是使用结构生物信息学工具从蛋白质的一级序列预测蛋白质的三级结构，然后将一种或多种底物分子对接到酶结构模型中。在过去的几年里,这些计算工具已经取得了重大进展，在使用物理方法解析结构之前，可以提供有关活性位点和酶-底物相互作用的有用信息。这里,以普通豆（菜豆）羟基肉桂酰辅酶A：四羟基己二酸羟基肉桂酰转移酶（HHHT）为例，我们描述了蛋白质结构预测和分子对接的方法和工作流程，这些方法和工作流程只能在个人计算机上使用开源工具进行。
