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Identifying foldable regions in protein sequence from the hydrophobic signal

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journal contribution
posted on 2008-02-01, 00:00 authored by C Pang, K Lin, Merridee Wouters, J Heringa, R George
Structural genomics initiatives aim to elucidate representative 3D structures for the majority of protein families over the next decade, but many obstacles must be overcome. The correct design of constructs is extremely important since many proteins will be too large or contain unstructured regions and will not be amenable to crystallization. It is therefore essential to identify regions in protein sequences that are likely to be suitable for structural study. Scooby-Domain is a fast and simple method to identify globular domains in protein sequences. Domains are compact units of protein structure and their correct delineation will aid structural elucidation through a divide-and-conquer approach. Scooby-Domain predictions are based on the observed lengths and hydrophobicities of domains from proteins with known tertiary structure. The prediction method employs an A*-search to identify sequence regions that form a globular structure and those that are unstructured. On a test set of 173 proteins with consensus CATH and SCOP domain definitions, Scooby-Domain has a sensitivity of 50% and an accuracy of 29%, which is better than current state-of-the-art methods. The method does not rely on homology searches and, therefore, can identify previously unknown domains.

History

Journal

Nucleic acids research

Volume

36

Issue

2

Pagination

578 - 588

Publisher

Oxford University Press

Location

Oxford, England

ISSN

0305-1048

eISSN

1362-4962

Language

eng

Notes

Reproduced with the kind permission of the copyright owner.

Publication classification

C1.1 Refereed article in a scholarly journal

Copyright notice

2007, The Authors

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