Zawaira, AShibayama, Y2014-04-292014-04-292012-12Zawaira, A and Shibayama, Y. 2012. A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs. J Struct Funct Genomics, vol. 13(4), pp 185-2001345-711Xhttp://download.springer.com/static/pdf/52/art%253A10.1007%252Fs10969-012-9141-7.pdf?auth66=1398588008_54b9d5387699d18617767a2405e199df&ext=.pdfhttp://hdl.handle.net/10204/7376Copyright: 2012 Springer Verlag. This an ABSTRACT ONLY. The definitive version is published in J Struct Funct Genomics, vol. 13(4), pp 185-200The 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.enFunctional genomicsSequence similaritySequence identityHomologyFold recognitionProtein interfaceArticleZawaira, A., & Shibayama, Y. (2012). A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs. http://hdl.handle.net/10204/7376Zawaira, A, and Y Shibayama "A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs." (2012) http://hdl.handle.net/10204/7376Zawaira A, Shibayama Y. A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs. 2012; http://hdl.handle.net/10204/7376.TY - Article AU - Zawaira, A AU - Shibayama, Y AB - 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. DA - 2012-12 DB - ResearchSpace DP - CSIR KW - Functional genomics KW - Sequence similarity KW - Sequence identity KW - Homology KW - Fold recognition KW - Protein interface LK - https://researchspace.csir.co.za PY - 2012 SM - 1345-711X T1 - A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs TI - A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs UR - http://hdl.handle.net/10204/7376 ER -