Bioinformatics Links Directory : Interactions, Pathways, Enzymes

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

KAAS - (Found July 2, 2008 )

KAAS (KEGG Automatic Annotation Server) is a tool for ortholog assignment and pathway mapping. KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.
http://www.genome.jp/kegg/kaas/

Pathway Miner - (Found July 2, 2008 )

Pathway Miner is a tool for searching lists of genes for associations in known pathway data from KEGG, BioCarta, and GenMAPP. Also provides statistical analyses.
http://www.biorag.org/pathway.html

PFP - (Found July 2, 2008 )

PFP (Patch Finder Plus) is a tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.
http://pfp.technion.ac.il/

The Osprey Network Visualization System - (Found July 2, 2008 )

Application for graphically representing physical and genetic biological interactions; is coupled with the General Repository of Interaction Datasets (The GRID); available for Unix and Windows.
http://biodata.mshri.on.ca/osprey

STRING - (Found July 2, 2008 )

STRING (Search Tool for the Retrieval of Interacting GenesProteins) is a protein-protein interactionassociation database. Both known and predicted interactions are included. The interactions are derived from existing data sources and literature and from high-throughput experiments. Predictions are also made based on an analysis of genomic context.
http://string.embl.de/

SLiMDisc - (Found July 2, 2008 )

SLiMDisc (Short Linear Motif Discovery) is a tool for finding shared motifs in proteins with a common attribute such as sub-cellular location or a common interaction partner.
http://bioware.ucd.ie/~slimdisc/

SiteEngine - (Found July 2, 2008 )

SiteEngine is a server that searches protein structures for regions that can potentially function as binding sites by scanning for regions on the surface of one protein structure that resemble a specific binding site on the other.
http://bioinfo3d.cs.tau.ac.il/SiteEngine/

SH3-Hunter - (Found July 2, 2008 )

SH3-Hunter identifies putative SH3 domain interaction sites on protein sequences.
http://cbm.bio.uniroma2.it/SH3-Hunter/

ProMateus - (Found July 2, 2008 )

ProMateus extends ProMate, a protein binding site predictor, and allows the user to suggest new features that might improve the prediction of the binding site locations.
http://bioportal.weizmann.ac.il/promate/

PRISM - (Found July 2, 2008 )

PRISM (PRotein Interactions by Structural Matching) is a tool for analysing protein interfaces and predicting protein-protein interactions.
http://gordion.hpc.eng.ku.edu.tr/prism/