APORC Document Center: InferPPI

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InferPPI: Predicting protein interactions based on parsimony tendency of domain interactions

Version 1.0
Last updated: September 23, 2006

Reference#

Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu, Yong Wang, Shihua Zhang, Luonan Chen. Predicting protein interactions based on parsimony tendency of domain interactions. Manuscript, 2006.

Method#

InferPPI aims to infer protein-protein interaction based on the parsimony principle of domain-domain interactions. Specifically, inferring domain interactions is a first step and formulated as an integer linear programming with different searching degree of training protein interaction. Then the model is solved by relaxed linear programming. By using the obtained domain interactions, novel protein interactions can be predicted by a formula. In contrast to probabilistic algorithms, InferPPI is an algorithm based on a deterministic model.　

Procedure#

InferDDI.exe: filename1 filename2 sd

This software is to inferring domain-domain interactions from training protein interactions, where filename1 is an input file containing protein interactions and filename2 is another input file containing the protein-domain relationships. Their format can be referred to the examples in InferDDI.zip. sd is a float number between 0 and 1 denoting the searching degree i.e. the proportion of protein interactions that take part in the training. A file named filename1.sd.dint containing putative domain interactions will be generated. This software is intended for those who only want to know putative domain interactions and do not care novel protein interaction.

InferPPI.exe: filename1 filename2 filename3 sd

This software is to inferring novel protein-protein interactions from a training set, where filename1 is the given protein interactions and filename2 is the corresponding protein-domain relationship information. Filename3 is a test set and you want to know if the protein pairs in this set have interactions. The implication of sd is the same as above. A file named filename3.sd.pint which containing interacting protein pairs in the test set will be returned. The format of all files can be referred to the examples in InferPPI.zip.