INTER-PROTEIN CONTACT PREDICTION (i-Patch) Package (Webpage Tool)
2009-09-25
This program is used to predict the inter-protein (domain) contact sites by using the amino acid propensity, pair propensity, triangle propensity of the interface, as well as the structure information for each contacting partner. The main function is IPCoP.m. This package is free of use, but the authors do not guarantee bug free of this package. Please feel free to contact the author with any comments, or suggestions. The primary reference for the present package is “R. Hamer(#), Qiang Luo(#), J.P. Armitage, G. Reinert, C.M. Deane(*). i-Patch: Inter-Protein Contact Prediction using Local Network Information. Proteins: Structure,Function, and Bioinformatics. October 2010, 78(13):2781--2797. ", which should be cited whenever this toolbox is used. Please find more information in the readme.pdf.
1 Main I/O of the package
Input: Multiple Sequence Alignmen (MSA) for two domains/proteins and the corresponding PDB files of the reference sequences in the MSA.
This package can deal with non-continuous domains and can only predict the inter-domain/protein contact sites for two domains/proteins each time.
Output: Five different scores for each site of the MSA to be inter-domain/protein contact site
2 Other features
1) get the top N predictions or the predictions given by score cutoff
2) generate the residue numbers of the predictions for display in Pymol
3) make the sequence file and feature files for view the result in Jalview
4) the low entropy sites can also be marked on the alignment in Jalview
5) find the real inter-chain contact sites in a big complex from a PDB file
3 Supplementary Data
Please also find some supplementary materials of the paper below:
1) the MSA and PDB files for Blind Test data set and the list of proteins -- blindtestdata.zip &Table S4
2) the MSA and PDB files for Fitting data set and the list of proteins -- fittingdata.zip & Table S3
3) the Matlab code to run i-Patch on the Blind Test data set -- DemoForTest.m
4) the Matlab code to run i-Patch on the Fitting data set -- DemoForFit.m