MDCinfer: PPI prediction tool based on multiple domain cooperation analysis

• Version 1.0
• Last updated: August 26, 2007

Reference#

• Rui-Sheng Wang, Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen. Analysis on multi-domain cooperation for predicting protein-protein interactions. BMC Bioinformatics, Vol. 8, 391, 2007.

Method#

MDCinfer aims to infer protein-protein interaction by considering cooperative domain interactions. Unlike most existing methods, it assumes cooperative-domain pairs but not only single-domain pairs as the basic units of a protein interaction. The interaction probabilities of single-domain pairs and cooperative-domain pairs are computed by a linear programming algorithm and a fast association probabilistic method. Novel protein interactions can be predicted by an extended probabilities model which can accommodate cooperative-domain pairs.

Procedure#

MDCinfer.exe Filename1 Filename2 Filename3 Negnum Methstr

This software is to predict novel protein-proteins interactions from training protein interactions, where Filename1 is an input file containing protein interactions which will act as a training set. Its format can be referred to an example called train.txt in MDCinfer.rar and Filename2 is another input file containing the test set, i.e. the protein pairs whose interaction states you want to know based on the training set. Also its format can be referred to an example called test.txt in MDCinfer.rar. Filename3 is a file containing the protein-domain relationships for the proteins in filename2 and its format can be referred to a file called testdomain.txt in MDCinfer.rar. Negnum is an integer number and indicates how many negative samples you want to add during training. Methstr is a string denoting which method you want to choose. It can only take two values: APMM denotes the fast association probabilistic method based on multi-domain cooperation, and LPM denotes the linear programming algorithm based on multi-domain cooperation.

Software#

This is a beta version of the program for preliminary testing. The program is still under development.

• MDCinfer.rar

Supplementary Materials#

• Numeriacal PPI data: Ito et al., 2001, Krogan et al., 2006
• Binary PPI data: (From Liu et al., 2005) yeast, worm, fly, domain information
• PPI data of multiple species in DIP: (From Riely et al., 2005) PPI data, Proteins, Domains
• Predicted DDIs on DIP data: APMM(1) APMM(2)
• Overlap with iPfam (top 3005) APMM(1) APMM(2)
• All the cooperative-domain interactions in MIPS
• All the cooperative-domain interactions in DIP
• All the cooperative-domain interactions in Krogan data set
• All the cooperative-domain interactions verified by complex in PDB