BioNetGen

Michael Blinov, James Faeder and William Hlavacek

A general-purpose tool for computer-aided generation of rule-based deterministic or stochastic models of chemical reaction systems that account for the full spectrum of microscopic species implied by specified activities, potential modifications and interactions of the domains of signaling molecules.

ReceptorDB

Michael Blinov and William Hlavacek

ReceptorDB, a service of the CellSignaling Team of the Theoretical Biology and Biophysics Group at the Los Alamos National Lab, provides access to models for ligand-receptor interactions. These models are essential for understanding receptor-mediated cellular responses to environmental changes, as ligand-receptor binding is the first step in receptor signaling. Models are encoded in electronic exchange, XML (eXtensible Markup Language)-based formats: SBML - System Biology MarkUp Language and MathML - Mathematical MarkUp Language.

EcoTFs database

Michael Wall and William Hlavacek

EcoTFs database catalogues data about autoregulation of transcription factors (TFs) in Escherichia coli and the molecular signals that affect the activities of these TFs.

Kinase Structural Models

Ben McMahon

Database of protein kinase function, based on currently available sequence and structural information. The clickable-dendrogram is from "The protein kinase complement of the human genome" Manning, G; Whyte, DB; Martinez, R; Hunter, T; Sudarsanam, S SCIENCE; DEC 6 2002; v.298, no.5600, p.1912, and is used with the permission of the authors.