Exploring Chemical Biosynthetic Design Space with Transform-MinER.
Exploring Chemical Biosynthetic Design Space with Transform-MinER.
复制标题
使用 Transform-MinER 探索化学生物合成设计空间。
DOI：
10.1021/acssynbio.9b00105
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发表时间：
2019
影响因子：
4.7
通讯作者：
J. Thornton
中科院分区：
文献类型：
--
作者：
Jonathan D. Tyzack;António J. M. Ribeiro;N. Borkakoti;J. Thornton
Transform-MinER（Transforming Molecules in Enzyme Reactions）是一个促进化学生物合成空间探索的网络应用程序，引导用户从酶设计项目或定向进化实验的有希望的起点开始。有两种类型的搜索是可能的：分子搜索允许用户提交一个源底物，使Transform-MinER搜索作用于类似底物的酶反应;而路径搜索还允许用户提交一个目标分子，使Transform-MinER搜索作用于类似底物的酶反应路径，以链接源和目标。Transform-MinER在源底物中搜索潜在的反应中心，并使用化学信息学指纹来识别那些位于与天然对应物相似的分子环境中的反应中心，在搜索空间的探索中，使用与天然反应最相似的反应来优先考虑更接近目标的步骤。介绍了Transform-MinER背后基于配体的方法，并对其性能进行了验证，获得了90%的成功率：首先，基于KEGG数据库中的天然途径数据集;其次，基于从头酶反应数据集。
Transform-MinER (Transforming Molecules in Enzyme Reactions) is a web application facilitating the exploration of chemical biosynthetic space, guiding the user towards promising start points for enzyme design projects or directed evolution experiments. Two types of search are possible: Molecule Search allows a user to submit a source substrate enabling Transform-MinER to search for enzyme reactions acting on similar substrates; whereas Path Search additionally allows a user to submit a target molecule enabling Transform-MinER to search for a path of enzyme reactions acting on similar substrates to link source and target. Transform-MinER searches for potential reaction centers in the source substrate and uses chemoinformatic fingerprints to identify those that are situated in molecular environments similar to native counterparts, prioritizing steps that move closer to the target using reactions most similar to native in its exploration of search space. The ligand-based methodology behind Transform-MinER is presented and its performance is validated yielding 90% success rates: firstly, on a data set of native pathways from the KEGG database; and secondly, on a data set of de novo enzyme reactions.
扩展酶的宇宙：通过机制引导的定向进化来访问非自然反应。
影响因子：
16.6
作者：
Renata, Hans;Wang, Z. Jane;Arnold, Frances H.
通讯作者：
Arnold, Frances H.