BIPS: BIANA Interolog Prediction Server. A tool for protein–protein interaction inference

Structural Bioinformatics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine (PRBB), 08003 Barcelona, Catalonia, Spain.
Nucleic Acids Research (Impact Factor: 9.11). 06/2012; 40(Web Server issue):W147-51. DOI: 10.1093/nar/gks553
Source: PubMed


Protein–protein interactions (PPIs) play a crucial role in biology, and high-throughput experiments have greatly increased
the coverage of known interactions. Still, identification of complete inter- and intraspecies interactomes is far from being
complete. Experimental data can be complemented by the prediction of PPIs within an organism or between two organisms based
on the known interactions of the orthologous genes of other organisms (interologs). Here, we present the BIANA (Biologic Interactions
and Network Analysis) Interolog Prediction Server (BIPS), which offers a web-based interface to facilitate PPI predictions
based on interolog information. BIPS benefits from the capabilities of the framework BIANA to integrate the several PPI-related
databases. Additional metadata can be used to improve the reliability of the predicted interactions. Sensitivity and specificity
of the server have been calculated using known PPIs from different interactomes using a leave-one-out approach. The specificity
is between 72 and 98%, whereas sensitivity varies between 1 and 59%, depending on the sequence identity cut-off used to calculate
similarities between sequences. BIPS is freely accessible at

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    • "A total of 631 933 positive pairs and 13 543 217 negative pairs were used for assessing giant panda networks, and 463 223 positive pairs and 13 111 432 negative pairs were used for assessing soybean networks. We compared the quality of the orthology-based networks by JiffyNet and BIPS, another public web server capable of constructing orthology-based protein networks (10), using identical query protein sequence input data. The BIPS web server differs substantially from JiffyNet as described above. "
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