:: DESCRIPTION
PIPINO is a software package to facilitate the identification of protein-protein interactions from affinity purification mass spectrometry data.
::DEVELOPER
BioInformatics Group Mittweida
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Profppikernel uses an accelerated version of the original profile kernel to train SVM based protein-protein interaction (PPI) prediction models and to predict new PPIs from sequence alone.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Evolutionary profiles improve protein-protein interaction prediction from sequence.
Hamp T, Rost B.
Bioinformatics. 2015 Feb 4. pii: btv077.
:: DESCRIPTION
DynaFace predicts obligatory and non-obligatory interactions among a set of 300 putative protein complexes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
NO
:: MORE INFORMATION
Citation:
DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex’s Dynamics.
Soner S, Ozbek P, Garzon JI, Ben-Tal N, Haliloglu T.
PLoS Comput Biol. 2015 Oct 27;11(10):e1004461. doi: 10.1371/journal.pcbi.1004461.
:: DESCRIPTION
DeNovo is a sequence-based negative sampling and machine learning framework that learns from PPIs of different viruses to predict for a novel one, exploiting the shared host proteins.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
DeNovo: Virus-Host Sequence-Based Protein-Protein Interaction Prediction.
Eid FE, ElHefnawi M, Heath LS.
Bioinformatics. 2015 Dec 16. pii: btv737.
:: DESCRIPTION
The PPI-PS method consists of a representation of each protein sequence by a vector of pairwise similarities against large subsequences of amino acids created by a shifting window which passes over concatenated protein training sequences.
::DEVELOPER
Nazar Zaki , Bioinformatics Laboratory, UAE University.
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2009 May 17;10:150. doi: 10.1186/1471-2105-10-150.
Protein-protein interaction based on pairwise similarity.
Zaki N, Lazarova-Molnar S, El-Hajj W, Campbell P.
:: DESCRIPTION
Strike (String Kernel) is a program which classifies protein-protein interaction into “interacting” and “non-interacting” sets based solely on amino acid sequence information. The classification is made by applying the string kernel technique. Two proteins are classified “interacting” if they contain similar subsequences of amino acids.
::DEVELOPER
Nazar Zaki , Bioinformatics Laboratory, UAE University.
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Adv Exp Med Biol. 2011;696:263-70. doi: 10.1007/978-1-4419-7046-6_26.
Strike: a protein-protein interaction classification approach.
Zaki N, El-Hajj W, Kamel HM, Sibai F.
:: DESCRIPTION
ITI project [Interactome-Transcriptome Integration] is a network-based robust classification of transcription profiles in cancer by large scale data integration of protein-protein interaction with DNA microarray data.
::DEVELOPER
The CRCM’s Integrative Bioinformatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Mar 1;28(5):672-8. doi: 10.1093/bioinformatics/bts025.
Interactome-transcriptome integration for predicting distant metastasis in breast cancer.
Garcia M, Millat-Carus R, Bertucci F, Finetti P, Birnbaum D, Bidaut G.
:: DESCRIPTION
PrePPI is a database of predicted and experimentally determined protein-protein interactions (PPI) for yeast and human. Predicted interactions in the database are determined using a Bayesian framework that combines structural, functional, evolutionary and expression information.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
PrePPI: a structure-informed database of protein-protein interactions.
Zhang QC, Petrey D, Garzón JI, Deng L, Honig B.
Nucleic Acids Res. 2013 Jan;41(Database issue):D828-33. doi: 10.1093/nar/gks1231.
:: DESCRIPTION
PIPs is a database of predicted human protein-protein interactions. The predictions have been made using a na?ve Bayesian classifier to calculate a Score of interaction.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
NO
:: MORE INFORMATION
Citation
PIPs: human protein–protein interaction prediction database
Mark D. McDowall, Michelle S. Scott and Geoffrey J. Barton
Nucl. Acids Res. (2009) 37 (suppl 1): D651-D656. doi: 10.1093/nar/gkn870
:: DESCRIPTION
LR_PPI is a web server for large-scale prediction of human protein-protein interaction from amino acid sequence based on latent topic feature
::DEVELOPER
Computational Systems Biology Group, Shanghai Jiao Tong University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
J Proteome Res. 2010 Oct 1;9(10):4992-5001. doi: 10.1021/pr100618t.
Large-scale prediction of human protein-protein interactions from amino acid sequence based on latent topic features.
Pan XY1, Zhang YN, Shen HB.