InteractoMIX is a suite of computational tools designed to exploit interactomics information at different levels ranging from genome-wide interactomes to their atomic 3D structural details.
Bionet is intended to provide a computational tool for modeling biological pathways or biosystem dynamics on multiple scales. At this time, manual descriptions of gene and protein interactions are described in text files with a simple format.The methodology in bionet is distinguished from previous qualitative modeling approaches in several ways. The goal was to develop a model that would allow experimental biologists to use the kind of qualitative data found in typical journal articles to describe the interaction of genes, proteins, and other cellular components to create computer models of large numbers of interacting parts. This arose from a practical need in our research to keep track of myriad components in pathway models that were built from data extracted from dozens of journal articles. Biologists already do this kind of mental modeling every time they make a new hypothesis; a tool was needed to aid in this reasoning. Secondly, with new sources of data becoming available, it was important to design a methodology that could be expanded in the future to integrate new data sources to refine models.
The BRAIN (Biologically Relevant Analysis of Interaction Networks) is a set of algorithms for predicting and analyzing protein domain-peptide ligand interactions based on experimentally known binding evidence (e.g. from protein chip or phage display experiments). BRAIN can be accessed as a Cytoscape plugin which reads peptide binding profiles and generates interactions displayed as a Cytoscape network.