Bioinformatics Links Directory : Interactions, Pathways, Enzymes

These links include databases for enzyme, metabolic and proteomic pathways. Many of these resources contain dynamic pathway diagrams.

PredBALBc - (Found July 2, 2008 )

PredBALBc is a tool that will predict MHC binding peptides in your protein sequence of interest for the H2d haplotype of the BALBc mouse.
http://antigen.i2r.a-star.edu.sg/predBalbc/

POPSCOMP - (Found July 2, 2008 )

POPSCOMP is a system for analysing the interaction between components of complexes based on calculations of the accessible surface that is buried when the complex is formed.
http://ibivu.cs.vu.nl/programs/popscompwww/

PIC - (Found July 2, 2008 )

Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions; such as disulphide bonds, hydrophobic interactions, hydrogen bonds, aromatic interactions, and ionic interactions within a protein or between proteins in a complex.
http://crick.mbu.iisc.ernet.in/~PIC/

iSPOT - (Found July 2, 2008 )

iSPOT (Sequence Prediction Of Target) uses experimental interaction data combined with structural residue-residue contact information to predict the peptide binding specificity of SH3, PDZ, and WW domains.
http://cbm.bio.uniroma2.it/ispot/

InterWeaver - (Found July 2, 2008 )

InterWeaver is a tool employing two approaches to detect potential protein interactions by searching for and interpreting evidence available from on-line databases. The first approach finds homologues for a sequence and searches for interacting partners in protein interaction and literature databases, and the second finds sequence domains, and then searches for domain fusion events and possible domain interactions.
http://interweaver.i2r.a-star.edu.sg/

Reactome - a knowledgebase of biological processes - (Found July 2, 2008 )

Reactome is a database of human biological pathways and processes ranging from basic processes of metabolism to complex regulatory pathways. The data is curated by biologists and subsequently peer-reviewed for accuracy and consistency. Cross-references with UniProt, PubMed, Ensembl, Gene Ontology and LocusLink are also provided. Reactome supersedes The Genome Knowledgebase project.
http://www.reactome.org/

firestar - (Found July 2, 2008 )

Firestar predicts functionally important residues, such as ligand binding sites, using structural templates and alignment reliability.
http://firedb.bioinfo.cnio.es/Php/FireStar.php

GenePath - (Found July 2, 2008 )

GenePath is a tool for automated construction of genetic networks and proposal of genetic experiments from mutant data.
http://www.genepath.org/genepath2

I2I-SiteEngine - (Found July 2, 2008 )

Interface-to-Interface (I2I)-SiteEngine compares pairs of interacting protein binding sites by recognizing similarity of physico-chemical properties and shapes in the protein-protein interfaces.
http://bioinfo3d.cs.tau.ac.il/I2I-SiteEngine/

iHOP - (Found July 2, 2008 )

iHOP (Information Hyperlinked over Proteins) allows researchers to explore a network of gene and protein interactions based on published scientific literature. For each gene search, iHOP reports sentences from abstracts associating it with other genes, links out to full abstracts, and reports experimental evidence for the interactions, if available. You can also select sentences to create and visualize your own gene model.
http://www.ihop-net.org/UniPub/iHOP/