Bioinformatics Links Directory : Interactions, Pathways, EnzymesThese links include databases for enzyme, metabolic and proteomic pathways. Many of these resources contain dynamic pathway diagrams.BioInfo3D- (Found July 2, 2008 ) BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.http://bioinfo3d.cs.tau.ac.il/ BRENDA - The Comprehensive Enzyme Information System- (Found July 2, 2008 ) Information about reaction and specificity, post-translational modifications, structure, stability, and references to other databases; free for academics.http://www.brenda.uni-koeln.de/ CNplot: Visualization of Pre-Clustered networks- (Found July 2, 2008 ) CNplot is a network visualization tool that can be used for large-scale networks, as long as they are pre-clustered.http://csb.stanford.edu/~nbatada/VCN.html Cytoscape- (Found July 2, 2008 ) Cytoscape is a visualization platform for use with molecular interaction networks. Interaction data can be integrated with other state data such as gene expression profiles. The input to Cytoscape includes lists of interaction pairs, and tabspace delimited files containing mRNA expression profiles. The nodes of the interaction networks can be filtered by such variables as GO annotations and number of interactions.http://www.cytoscape.org/ CytoSVM- (Found July 2, 2008 ) CytoSVM is a Support Vector Machine (SVM) based server that predicts putative cytokine-receptor interactions based on a primary protein sequence. Using this method, results from screening the human and mouse genomes are available via a database search.http://bioinf.xmu.edu.cn/software/cytosvm/cytosvm.php DILIMOT- (Found July 2, 2008 ) Discovery of Linear Motifs (DILIMOT) is a server for finding short (3-8 amino acids) over-represented peptide patterns in a set of proteins.http://dilimot.embl.de/ DIP- (Found July 2, 2008 ) The Database of Interacting Proteins (DIP) allows users to search for interacting proteins. Results lists can be searched andor visualized (statically or dynamically). Users can submit new protein-protein interactions and update database entries.http://dip.doe-mbi.ucla.edu/ ENZYME - Enzyme nomenclature database- (Found July 2, 2008 ) Repository of enzyme nomenclature information; useful selection of cross references to other databases; free for research purposes only.http://us.expasy.org/enzyme/ 3D-partner- (Found July 2, 2008 ) 3D-partner is a tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes.http://gemdock.life.nctu.edu.tw/3D-partner/vers1/index.php |