Selenzyme: enzyme selection tool for pathway design
Selenzyme: enzyme selection tool for pathway design
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DOI：
10.1093/bioinformatics/bty065
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发表时间：
2018-06-15
期刊：
影响因子：
5.8
通讯作者：
Faulon, Jean-Loup
中科院分区：
文献类型：
--
作者：
Carbonell, Pablo;Wong, Jerry;Faulon, Jean-Loup
摘要：合成生物学将工程学原理应用于生物学，以创造自然界中前所未见的生物功能。合成生物学最令人兴奋的应用之一是设计新的生物体，能够以更环保的方式生产有价值的化学品，包括药物和生物材料；可持续时尚。然而，选择正确的酶来催化每个反应步骤以产生所需的目标化合物并非易事。在这里，我们推出 Selenzyme，一种用于代谢途径设计的免费在线酶选择工具。引导用户完成几个决策步骤，以便为给定的途径步骤列出最佳候选者。该工具基于现有数据库和工具以图形方式呈现有关酶的关键信息，例如：序列和催化反应的相似性；来源生物和预期宿主物种之间的系统发育距离；多重比对突出显示保守区域、预测的催化位点和活性区域以及相关特性，例如预测的溶解度和跨膜区域。 Selenzyme 为生物铸造厂的自动化工作流程提供定制序列选择。
A Summary: Synthetic biology applies the principles of engineering to biology in order to create biological functionalities not seen before in nature. One of the most exciting applications of synthetic biology is the design of new organisms with the ability to produce valuable chemicals including pharmaceuticals and biomaterials in a greener; sustainable fashion. Selecting the right enzymes to catalyze each reaction step in order to produce a desired target compound is, however, not trivial. Here, we present Selenzyme, a free online enzyme selection tool for metabolic pathway design. The user is guided through several decision steps in order to shortlist the best candidates for a given pathway step. The tool graphically presents key information about enzymes based on existing databases and tools such as: similarity of sequences and of catalyzed reactions; phylogenetic distance between source organism and intended host species; multiple alignment highlighting conserved regions, predicted catalytic site, and active regions and relevant properties such as predicted solubility and transmembrane regions. Selenzyme provides bespoke sequence selection for automated workflows in biofoundries.