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MDCinfer: PPI prediction tool based on multiple domain cooperation analysis

  • Version 1.0
  • Last updated: August 26, 2007

Reference#

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.

Supplementary Materials#


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List of attachments

Kind Attachment Name Size Version Date Modified Author Change note
txt
APMM1_iPfam.txt 3.4 kB 1 14-May-2011 21:23 LingyunWu
txt
APMM2_iPfam.txt 3.6 kB 1 14-May-2011 21:23 LingyunWu
txt
DDIbyAPMM1.txt 492.4 kB 1 14-May-2011 21:23 LingyunWu
txt
DDIbyAPMM2.txt 587.9 kB 1 14-May-2011 21:24 LingyunWu
xls
DIPCooperativeDomains.xls 1,190.4 kB 1 14-May-2011 21:21 LingyunWu
txt
FlyKnumNR.txt 30.5 kB 1 14-May-2011 21:24 LingyunWu
xls
KroganCooperativeDomains.xls 2,205.7 kB 1 14-May-2011 21:21 LingyunWu
txt
KroganYeastExtended.txt 270.5 kB 1 14-May-2011 21:24 LingyunWu
rar
MDCinfer.rar 373.1 kB 1 14-May-2011 21:23 LingyunWu
xls
MIPSCooperativeDomains.xls 256.5 kB 1 14-May-2011 21:21 LingyunWu
txt
RileyPPIs.txt 305.3 kB 1 14-May-2011 21:24 LingyunWu
txt
RileyProts.txt 277.6 kB 1 14-May-2011 21:24 LingyunWu
txt
Rileydoms.txt 185.1 kB 1 14-May-2011 21:24 LingyunWu
xls
StruCoopDom.xls 39.9 kB 1 14-May-2011 21:21 LingyunWu
txt
WormKnumNR.txt 45.7 kB 1 14-May-2011 21:25 LingyunWu
txt
YeastKnumNR.txt 33.1 kB 1 14-May-2011 21:25 LingyunWu
txt
all.format.do-pr.txt 379.4 kB 1 14-May-2011 21:23 LingyunWu
dat
ito-ppi.dat 49.6 kB 1 14-May-2011 21:21 LingyunWu
« This particular version was published on 14-May-2011 21:27 by LingyunWu.