Holliday Gemma L, Brown Shoshana D, Akiva Eyal, Mischel David, Hicks Michael A, Morris John H, Huang Conrad C, Meng Elaine C, Pegg Scott C-H, Ferrin Thomas E, Babbitt Patricia C
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.
Human Longevity, Inc, San Diego, CA 92121, USA.
Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/bax006.
With ever-increasing amounts of sequence data available in both the primary literature and sequence repositories, there is a bottleneck in annotating molecular function to a sequence. This article describes the biocuration process and methods used in the structure-function linkage database (SFLD) to help address some of the challenges. We discuss how the hierarchy within the SFLD allows us to infer detailed functional properties for functionally diverse enzyme superfamilies in which all members are homologous, conserve an aspect of their chemical function and have associated conserved structural features that enable the chemistry. Also presented is the Enzyme Structure-Function Ontology (ESFO), which has been designed to capture the relationships between enzyme sequence, structure and function that underlie the SFLD and is used to guide the biocuration processes within the SFLD.
随着原始文献和序列数据库中可用序列数据量的不断增加,在将分子功能注释到序列方面存在瓶颈。本文描述了结构-功能联系数据库(SFLD)中使用的生物编目过程和方法,以帮助应对一些挑战。我们讨论了SFLD中的层次结构如何使我们能够推断功能多样的酶超家族的详细功能特性,其中所有成员都是同源的,保留其化学功能的一个方面,并具有相关的保守结构特征以实现化学反应。还介绍了酶结构-功能本体(ESFO),它旨在捕捉构成SFLD基础的酶序列、结构和功能之间的关系,并用于指导SFLD内的生物编目过程。