Journal of Structural and Functional Genomics

, Volume 13, Issue 4, pp 185–200

A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs


DOI: 10.1007/s10969-012-9141-7

Cite this article as:
Zawaira, A. & Shibayama, Y. J Struct Funct Genomics (2012) 13: 185. doi:10.1007/s10969-012-9141-7


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.


Functional genomics Sequence similarity Sequence identity Homology Fold recognition Protein–protein interface 



Open reading frame




Protein–protein interactions

Supplementary material

10969_2012_9141_MOESM1_ESM.doc (787 kb)
Supplementary material 1 (DOC 787 kb)
10969_2012_9141_MOESM2_ESM.doc (58 kb)
Supplementary material 2 (DOC 57 kb)
10969_2012_9141_MOESM3_ESM.doc (34 kb)
Supplementary material 3 (DOC 33 kb)
10969_2012_9141_MOESM4_ESM.doc (32 kb)
Supplementary material 4 (DOC 32 kb)
10969_2012_9141_MOESM5_ESM.doc (542 kb)
Supplementary material 5 (DOC 541 kb)
10969_2012_9141_MOESM6_ESM.doc (1 mb)
Supplementary material 6 (DOC 1046 kb)
10969_2012_9141_MOESM7_ESM.doc (44 kb)
Supplementary material 7 (DOC 44 kb)
10969_2012_9141_MOESM8_ESM.doc (49 kb)
Supplementary material 8 (DOC 49 kb)
10969_2012_9141_MOESM9_ESM.doc (904 kb)
Supplementary material 9 (DOC 903 kb)
10969_2012_9141_MOESM10_ESM.doc (92 kb)
Supplementary material 10 (DOC 91 kb)
10969_2012_9141_MOESM11_ESM.doc (1.4 mb)
Supplementary material 11 (DOC 1460 kb)
10969_2012_9141_MOESM12_ESM.doc (1.7 mb)
Supplementary material 12 (DOC 1710 kb)
10969_2012_9141_MOESM13_ESM.doc (1.2 mb)
Supplementary material 13 (DOC 1254 kb)
10969_2012_9141_MOESM14_ESM.doc (44 kb)
Supplementary material 14 (DOC 44 kb)
10969_2012_9141_MOESM15_ESM.doc (33 kb)
Supplementary material 15 (DOC 33 kb)
10969_2012_9141_MOESM16_ESM.doc (60 kb)
Supplementary material 16 (DOC 61 kb)

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  1. 1.Gene Expression and Biophysics Group, Synthetic BiologyERAPretoriaSouth Africa

Personalised recommendations