Structure search & retrieval
Macromolecules
NIH Research Resource Center for the Development of Multiscale Modeling Tools for Structural Biology
http://mmtsb.org/
Search the Molecular Modeling Database (MMDB) at NCBI
http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure
World Index of Molecular Visualization Resources: Sources of PDB Files
http://molvis.sdsc.edu/visres/pdbs/titles.jsp
Small chemicals
PubChem provides information on the biological activities of small molecules.
http://pubchem.ncbi.nlm.nih.gov/
Search in 39 million indexed structures from over 80 databases (27 million unique structures)
http://cactus.nci.nih.gov/cgi-bin/lookup/search
Calculator Plugins are modules of ChemAxon's Marvin and JChem cheminformatics platforms which calculate physico-chemical properties from chemical structures. Calculator Plugins currently cover a range of life science related properties and the development of new plugins is ongoing.
http://www.chemaxon.com/marvin/help/calculations/calculator-plugins.html
NWU's Chemical and Safety relational database. This site is intended to serve faculty, staff, and student needs regarding local chemical and laboratory safety issues, chemical visualization, and other chemical or chemistry related information.
http://howard.nebrwesleyan.edu/classes/cs295/shoemaker/chem/index.php