Links Relevant to Computational Biochemistry

The first site to check out is:
Enzymes and MCA in Marseilles: Lots of useful material here and always up to date.

Software Sites

BioKin Enzyme kinetic software.
BioQuest Metabolic Simulation
DBSolve UK site Software for metabolic, enzymatic and receptor-ligand binding simulation.
E-Cell From a Japanese group who have a modeling and simulation environment for biochemical and genetic processes for the Linux platform.
Electronic Arc Experimental visual simulator
MetaModel Modeling Metabolic Pathways under MS-DOS
Pedro Mendes' Gepasi site, a popular bio/chemical simulator for Windows 32.
PathDB A database and discovery tool for biochemical pathways and metabolism
netBuilder A Windows based gene circuit simulator
ProMoT
Online Modeling System A web based modeling systems
JigCell Java based pathway simulator at Virginia tech (I know, two simulators in one university!)
bioSPICE DARPA funded biochemical pathway simulation software project.

Adam Arkin BioSpice etc
Biocomputing group at Wayne Stat Uni
BioPathways "Supporting the Transformation of Genomic Information into a Web of Knowledge for the Life Sciences"
David Fell's Research Group Details of the research carried out by the group and links to software.
Metatool main site (Elementary modes software)
Centre of Computational Biology and John Hopkins
Princeton Integrative Genomics New institute dedicated to integrative genomics
Published StandardsCellML A corporate standard for storing metabolic type data destined for numerical simulation
SBML Our very own standard for exchanging biochemical network models
BioPathways Consortium Corporate SitesEntelos Company which specializes in physiological modelling.
Physiome Sciences A company specialising in metabolic simulations (Part Supporter of CellML)
KineCyte by Daniel Cook, a visual pathway simulator for the Mac (Commercial, but nice)
Gene Network Sciences Claims to be able to model very large systems

Dr PR Butler, Department of Biomolecular Sciences, UMIST. A rather well presented and good introduction to metabolic control analysis.
Pedro Mendes' introduction to Metabolic Control Analysis
The MCA FAQ
Review from EJB Review which concentrates on Genetic and metabolic engineering with a rare but important emphasis on quantitative methods.
Computer Simulation of Metabolism
Interesting Artificial Chemistry research including Bio-Organisation.
Quantitative Modeling of Metabolic Networks This paper discusses the theory of Petrinets and how they might be useful for the quantitative modeling of biochemical networks.