小柯机器人

英国威康信托基因组园区Janet M. Thornton和Antonio J. M. Ribeiro共同合作，近期取得重要工作进展。他们研究开发了EzMechanism，一种提出酶反应催化机制的自动化工具。相关研究成果2023年9月21日在线发表于《自然—方法学》杂志上。

据介绍，多年来，使用实验和模拟方法研究了数百种酶反应机制。这些关于生物催化的丰富经验现在已经成熟，可以作为研究酶机制的新知识基础。

研究人员开发了一个工具，EzMechanism。这一工具能够自动推断出一个给定的三维活性位点和酶反应的机制路径，基于机制和催化位点图谱(一个酶机制数据库)编译的一组催化规则。每个人都可以通过web用户界面使用EzMechanism（发音为“简易”机制）。在研究一种机制时，EzMechanism通过确保相关信息得到考虑，促进并改进假设的产生，这些信息来源于相关和非相关酶的文献。

最后，研究人员在62种酶上验证了EzMechanism工具，并确定了进一步改进的途径，包括需要更多通用的催化规则。

附：英文原文

Title: EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions

Author: Ribeiro, Antonio J. M., Riziotis, Ioannis G., Tyzack, Jonathan D., Borkakoti, Neera, Thornton, Janet M.

Issue&Volume: 2023-09-21

Abstract: Over the years, hundreds of enzyme reaction mechanisms have been studied using experimental and simulation methods. This rich literature on biological catalysis is now ripe for use as the foundation of new knowledge-based approaches to investigate enzyme mechanisms. Here, we present a tool able to automatically infer mechanistic paths for a given three-dimensional active site and enzyme reaction, based on a set of catalytic rules compiled from the Mechanism and Catalytic Site Atlas, a database of enzyme mechanisms. EzMechanism (pronounced as ‘Easy’ Mechanism) is available to everyone through a web user interface. When studying a mechanism, EzMechanism facilitates and improves the generation of hypotheses, by making sure that relevant information is considered, as derived from the literature on both related and unrelated enzymes. We validated EzMechanism on a set of 62 enzymes and have identified paths for further improvement, including the need for additional and more generic catalytic rules.

DOI: 10.1038/s41592-023-02006-7

Source: https://www.nature.com/articles/s41592-023-02006-7

Nature Methods：《自然—方法学》，创刊于2004年。隶属于施普林格·自然出版集团，最新IF：47.99
官方网址：https://www.nature.com/nmeth/
投稿链接：https://mts-nmeth.nature.com/cgi-bin/main.plex