Document Detail

A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs.
MedLine Citation:
PMID:  22956349     Owner:  NLM     Status:  Publisher    
The study of the protein-protein interactions (PPIs) of unique ORFs is a strategy for deciphering the biological roles of unique ORFs of interest. For uniform reference, we define unique ORFs as those for which no matching protein is found after PDB-BLAST search with default parameters. The uniqueness of the ORFs generally precludes the straightforward use of structure-based approaches in the design of experiments to explore PPIs. Many open-source bioinformatics tools, from the commonly-used to the relatively esoteric, have been built and validated to perform analyses and/or predictions of sorts on proteins. How can these available tools be combined into a protocol that helps the non-expert bioinformaticist researcher to design experiments to explore the PPIs of their unique ORF? Here we define a pragmatic protocol based on accessibility of software to achieve this and we make it concrete by applying it on two proteins-the ImuB and ImuA' proteins from Mycobacterium tuberculosis. The protocol is pragmatic in that decisions are made largely based on the availability of easy-to-use freeware. We define the following basic and user-friendly software pathway to build testable PPI hypotheses for a query protein sequence: PSI-PRED → MUSTER → metaPPISP → ASAView and ConSurf. Where possible, other analytical and/or predictive tools may be included. Our protocol combines the software predictions and analyses with general bioinformatics principles to arrive at consensus, prioritised and testable PPI hypotheses.
Alexander Zawaira; Youtaro Shibayama
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-9-7
Journal Detail:
Title:  Journal of structural and functional genomics     Volume:  -     ISSN:  1570-0267     ISO Abbreviation:  J. Struct. Funct. Genomics     Publication Date:  2012 Sep 
Date Detail:
Created Date:  2012-9-7     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101128185     Medline TA:  J Struct Funct Genomics     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Gene Expression and Biophysics Group, Synthetic Biology, ERA, Building 20, CSIR Biosciences, Meiring Naude Road, Brummeria, Pretoria, 0001, South Africa,
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