NDLI: An integrated framework for functional annotation of protein structural domains

Content Provider	ACM Digital Library
Author	Deng, Lei Chen, Zhigang
Copyright Year	2015
Description	Author Affiliation: Central South University, Changsha, China(Chen, Zhigang; Deng, Lei)
Abstract	Structural domains are evolutionary and functional units of proteins and play a critical role in comparative and functional genomics. Computational assignment of domain function with high reliability is essential for understanding whole-protein functions. However, functional annotations are conventionally assigned onto full-length proteins rather than associating specific functions to the individual structural domains. In this article, we present Structural Domain Annotation (SDA), a novel computational approach to predict functions for SCOP structural domains. The SDA method integrates heterogeneous information sources, including structure alignment based protein-SCOP mapping features, InterPro2GO mapping information, PSSM Profiles, and sequence neighborhood features, with a Bayesian network. By large-scale annotating Gene Ontology terms to SCOP domains with SDA, we obtained a database of SCOP domain to Gene Ontology mappings, which contains ~162,000 out of the approximately 166,900 domains in SCOPe 2.03 (>97 percent) and their predicted Gene Ontology functions. We have benchmarked SDA using a single-domain protein dataset and an independent dataset from different species. Comparative studies show that SDA significantly outperforms the existing function prediction methods for structural domains in terms of coverage and maximum F-measure.
Starting Page	902
Ending Page	913
Page Count	12
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2015.2389213
Volume Number	12
Issue Number	4
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2015-07-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Bayesian network PSSM Scop domain function Structure alignment
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

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