Journal article
Functional classification of protein 3D structures from predicted local interaction sites
Journal of bioinformatics and computational biology, v 8 Suppl 1(supp01)
Dec 2010
PMID: 21155016
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
A new approach to the functional classification of protein 3D structures is described with application to some examples from structural genomics. This approach is based on functional site prediction with THEMATICS and POOL. THEMATICS employs calculated electrostatic potentials of the query structure. POOL is a machine learning method that utilizes THEMATICS features and has been shown to predict accurate, precise, highly localized interaction sites. Extension to the functional classification of structural genomics proteins is now described. Predicted functionally important residues are structurally aligned with those of proteins with previously characterized biochemical functions. A 3D structure match at the predicted local functional site then serves as a more reliable predictor of biochemical function than an overall structure match. Annotation is confirmed for a structural genomics protein with the ribulose phosphate binding barrel (RPBB) fold. A putative glucoamylase from Bacteroides fragilis (PDB ID 3eu8) is shown to be in fact probably not a glucoamylase. Finally a structural genomics protein from Streptomyces coelicolor annotated as an enoyl-CoA hydratase (PDB ID 3g64) is shown to be misannotated. Its predicted active site does not match the well-characterized enoyl-CoA hydratases of similar structure but rather bears closer resemblance to those of a dehalogenase with similar fold.
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Details
- Title
- Functional classification of protein 3D structures from predicted local interaction sites
- Creators
- Ramya Parasuram - Northeastern UniversityJoslynn S Lee - Northeastern UniversityPengcheng Yin - Northeastern UniversitySrinivas Somarowthu - Northeastern UniversityMary Jo Ondrechen - Northeastern University
- Publication Details
- Journal of bioinformatics and computational biology, v 8 Suppl 1(supp01)
- Publisher
- World Scientific Publishing
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Biochemistry and Molecular Biology
- Web of Science ID
- WOS:000208165500002
- Scopus ID
- 2-s2.0-78649986149
- Other Identifier
- 991020837743204721
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InCites Highlights
Data related to this publication, from InCites Benchmarking & Analytics tool:
- Web of Science research areas
- Biochemical Research Methods
- Computer Science, Interdisciplinary Applications
- Mathematical & Computational Biology