Tools


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)

Database
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.org : 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 semanticweb.org

Databases

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



Chem2Bio2RDF
ChEMBL

Other resource lists


OSDD list of computational resources
Chemical Information Sources Wiki
Cheminformatics.org
Netsci.org
ChemistrySoftwares Archive of chemistry softwares