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Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/bax006.

Biocuration in the structure-function linkage database: the anatomy of a superfamily.

Author information

1
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.
2
Human Longevity, Inc, San Diego, CA 92121, USA.
3
Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA.
4
Gladstone Institutes, San Francisco, CA 94158, USA.
5
California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA.

Abstract

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.

Database URL:

http://sfld.rbvi.ucsf.edu/.

PMID:
28365730
PMCID:
PMC5467563
DOI:
10.1093/database/bax006
[Indexed for MEDLINE]
Free PMC Article

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