Pathway databases and websites

Alliance for Cellular Signaling (AfCS) – Nature Gateway	Nature magazine	Electronic journal. Sounds like a pathway site, but isn’t.
Apoptosis Special Interest Site	Roche Diagnostics	Vendor website with detailed diagram of apoptosis pathway linked to products.
BioCarta	BioCarta	Vendor website of 285 annotated pathway diagrams linked to products.
Biological Biochemical Image Database (BBID)	Kevin Becker, National Institute on Aging, NIH	Collection of pathway diagrams from published papers.
Boehringer Mannheim - Biochemical Pathways	ExPASy, Swiss Institute of Bioinformatics	Online version of famous wall chart.
CellML Examples & Models	CellML.org (Physiome Sciences, Inc.)	Repository of ~125 models expressed in CellML mathematical formalism.
BioCyc (includes EcoCyc)	Peter Karp, SRI	Major database of E. Coli pathways. Umbrella BioCyc database has 477 pathways from several (mostly bacterial) species.
IUBMB-Nicholson Minimaps	Donald Nicholson, The University, Leeds, England	Online supplement to textbook with 26 diagrams of metabolic pathways.
Kyoto Encyclopedia of Genes and Genomes (KEGG)	Kyoto University Bioinformatics Center	Premier pathway database with more than 10,000 pathways.
Mammalian MAPK Signaling Pathways	James Woodgett, Princess Margaret Hospital, Toronto	Laboratory website with annotated diagram and text description of MAPK cascade.
SBML Model Repository	Maria Schilstra, University of Hertfordshire	Repository of 18 models expressed in SBML mathematical formalism.
Science Signal Transduction Knowledge Environment (STKE)	Science magazine	Electronic journal with 48 pathway diagrams, 14 of which are described in text perspectives.

Protein interaction databases

Biomolecular Interaction Network Database (BIND)	Chris Hogue, University of Toronto
Biomolecular Relations in Information Transmission and Expression (BRITE)	Kyoto University Bioinformatics Center
Database of Interacting Proteins (DIP)	David Eisenberg, University of California at Los Angeles
Molecular INTeraction database (MINT)	Gianni Cesareni, University of Rome
Human Protein Reference Database (HPRD)	Akhilesh Pandey, Johns Hopkins University

Categorized list of papers on analysis of protein interaction data

Standards and Interest Groups

BioPathways Consortium		Organizes conferences.
BioPAX : Biological Pathways Exchange		Focus on knowledge representation.
CellML	Co-development by Physiome and the Bioengineering Institute, University of Auckland	Mathematically oriented with focus on simulation and modeling.
Systems Biology Markup Language (SBML)	Associated with Systems Biology Workbench (SBW), ERATO Kitano Systems Biology Project	Mathematically oriented with focus on simulation and modeling.

Companies with simulation and modeling software

Cellnomica

Entelos

Gene Network Sciences

Genomatica

Kenna Technologies

Physiome Science

Companies with pathway drawing software

BioCarta (free Freehand templates)

Stratagene (partnership with Iobion)