title: A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs.
abstract: 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.
authors.affiliation: Gene Expression and Biophysics Group, Synthetic Biology, ERA, CSIR Biosciences, Brummeria, Pretoria, South Africa. azawaira@gmail.com
authors.forename: Alexander
authors.initials: A
authors.lastname: Zawaira
authors.forename: Youtaro
authors.initials: Y
authors.lastname: Shibayama
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D017793:Luteovirus / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009169:Mycobacterium tuberculosis / Q000737:chemistry*; D016366:Open Reading Frames; D017510:Protein Folding; D025941:Protein Interaction Mapping / Q000379:methods; D017433:Protein Structure, Secondary; D015203:Reproducibility of Results; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software; D014764:Viral Proteins / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D014764:Viral Proteins