![]() By combining different peptide and protein features using multiple Bayesian models we are able to predict high confidence interactions with an overall accuracy accuracy of 0.97Īvailable from the Domo-Pred Yeast homepageĭoMo-Pred Human is a novel method of predicting SH3 domain-peptide mediated protein-protein interactions in humans using phage display data. This method uses position weight matrix models of protein linear motif preference for individual SH3 domains to scan the proteome for potential hits and then filters these hits using a range of evidence sources related to sequence-based and cellular constraints on protein interactions. Sequence logos and logo trees can be saved in various formats including PDF, PNG, and JPEG.ĭoMo-Pred Yeast is a novel method for predicting physiologically relevant SH3 domain-peptide mediated protein-protein interactions in S. You can also generate "logo trees" based on clustered protein profiles to analyze binding motif classes. LOLA allows you to generate custom sequence logos by setting parameters such as logo height, trim percentage, and residue colour scheme. LOLA (LOgos Look Amazing) is a tool for generating sequence logos using Position Weight Matrix based protein profiles. BRAIN can be accessed as a Cytoscape plugin which reads peptide binding profiles and generates interactions displayed as a Cytoscape network. from protein chip or phage display experiments). The Biologically Relevant Analysis of Interaction Networks (BRAIN) is a set of algorithms for predicting and analyzing protein domain-peptide ligand interactions based on experimentally known binding evidence (e.g. For instance, clusters in a protein-protein interaction network are often protein complexes and parts of pathways, while clusters in a protein similarity network represent protein families. Clusters mean different things in different types of networks. MCODE is a Cytoscape plugin that finds clusters (highly interconnected regions) in a network. Released by: Ferro, Giugno, Pulvirenti group, University of Catania, Bader group, University of Toronto and Shasha group, New York University.Īvailable from the Bader Lab mirror of the NetMatch homepage Node and edge attributes of any type and paths of unknown length can be specified in the search. NetMatch is a Cytoscape plugin that finds user defined network motifs in any Cytoscape network. Plugins may be developed using the Cytoscape open Java software architecture by anyone and plugin community development is encouraged.Ĭytoscape was originally developed at the Institute of Systems Biology and is now a collaborative effort involving many different academic and commercial groups.įun link: Controlling Cytoscape using the Nintendo Wiimote Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases. ![]() Additional features are available as plugins.
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