Programming / statistical environments and pipelining
R - statistical computing package including clustering and predictive modeling. Has been extended for cheminformatics with RCDK
Orange - statistical computing and workflow package extended for cheminformatics / QSAR with AZCompTox/AZOrange (see JChemInf paper)
ChemMine cheminformatics workbench
Knime - pipelining / workflow and visualization tool for cheminformatics
CDK - Chemistry Development Kit - Java toolkit for cheminformatics
OpenBabel - Open Source Chemistry Tookbox (see JChemInf paper)

OrChem - chemistry cartridge for Oracle that uses the CDK (see JChemInf paper)

Visualization and navigation
Cytoscape - network visualization and analysis tool - extended for cheminformatics by ChemViz and DrugViz
Gephi Gephi is an interactive visualization and exploration platformfor all kinds of networks and complex systems, dynamic and hierarchical graphs.
Graph Insight: GraphInsight is a visualization software that lets you explore graph data through high quality interactive representations.
Weave(web based data Visualization) Weave (BETA 1.0) is a new web-based visualization platform designed to enable visualization of any available data by anyone for any purpose. Weave is an application development platform supporting multiple levels of user proficiency – novice to advanced – as well as the ability to integrate, disseminate and visualize data at “nested” levels of geography. : Processing is an open source programming language and environment for people who want to create images, animations, and interactions. Initially developed to serve as a software sketchbook and to teach fundamentals of computer programming within a visual context, Processing also has evolved into a tool for generating finished professional work.
D3.js : D3.js is a small, free JavaScript library for manipulating documents based on data.
XGOBI : Software for multivariate data visualization
ESOM(Databionic) : The Databionic ESOM Tools is a suite of programs to perform data mining tasks like clustering, visualization, and classification with Emergent Self-Organizing Maps (ESOM). Features include:

Online tools
UNM Biocomputing tools including bioactivity data mining, clustering, depiction, format conversion, drug-likeness and many more tools
Molinspiration - Molecular property (including LogP) and activity prediction

Semantic Web
D2R- converting relational database to RDF
Virtuoso-Triple store,
Protege- OWL editor
Exhibit- XML, JSON visualization

Semantic Web Development Tools
Semantic Web tools on


Sixty four free chemistry database listed in Depth First (covered pretty much all the public database), highlight some of them:
PubChem- definitely the biggest one, as Jan 2011, PubChem includes 31 million entries.
Chemspider- covers over 26 million structures as Nov 2011, high quality data and with many detailed properties
ChEBI- focuses on the ontology of chemical compounds
DrugBank- Drug resources
ZINC - commercial compounds for virtual screening, contains over 13 million
ChemBank -
eMolecules “eMolecules discovers sources of chemical data by searching the Internet, and receives submissions from data providers such as chemical suppliers and academic research institutions.”
KEGG: it is not free now


Other resource lists

OSDD list of computational resources
Chemical Information Sources Wiki
ChemistrySoftwares Archive of chemistry softwares