The following websites are just some of those that I find useful in my work:
Collections of Collections
The Nucleic Acids Research database issue 2012 many, many databases with a strong biology bias – again far too many to summarise here
An excellent compilation of a host of in silico resources for drug design is particularly welcome and here it is. For the full reference summary visit this Drug Discovery Today article. The authors also highlight several other compilations including; Bioinformatics Links Directory which “features curated links to molecular resources, tools and databases”; Click2Drug with 733 links relating to drug design.. Cheminformaticvs and molecular modelling has its own compilation from Dr Kwang with about 931 links
From the Chemspider home page:
ChemSpider is a free-to-access curated annotated collection of compound data from across the web, provided for the benefit of the community by the Royal Society of Chemistry (RSC).
Includes ACD and Chemaxon property prediction tools.
CWM Global Search searches the Internet by structure, synonym, CAS Registry Number and free text. CWM Global Search presently searches more than 60 free chemical and pharma relevant databases — containing more than 100 million pages which associate chemical structures with data.
The PDB for protein crystallography.
PDBWiki A community annotated knowledge base of biological molecular structures.
The Structural Biology Database for information about structural biology and structural genomics.
The Cambridge Crystallographic database now with over 500,000 crystal structures.
Molecular Modelling – Viewers
“Fieldview from Cresset is a molecular viewer/editor designed to create, modify, view and compare molecules along with their associated Field patterns and physicochemical properties.” Download is free.
The Accelrys DS Visualizer is an unsupported free download from Accelrys for viewing small molecules proteins and protein ligand interactions.
Sets of Biological Data
Pubchem is a public, web-accessible database to search for biological data by assay or by compound.
Chembl with nearly 11 million curated activities on 1.3 million compounds and 10,000 targets an important resource.
DrugBank A bioinformatics and cheminformatics database containing data (e.g. target activity and target sequence ) on approved and experimental drugs small molecule and protein/peptides.
Cansar Specifically targeted biological data associated with oncology targets from Cancer Research UK.
Experimentally measured binding affinities for ligands bound to crystal structures.
STITCH is a resource to explore known and predicted interactions of chemicals and proteins
Compounds to Purchase
Zinc A free searchable database of upto 13M purchasable compounds in 3D format ready for docking.
eMolecules a collection of 8 million molecules available for purchase free for basic searches.
Molport has 9 million compounds available through something over 200 suppliers.
Biology, BiX Related
National Centre for Biological Information essential resource with multiple links to important BiX databases.
Pathway interaction database – mapping of many biological pathways.
Confused by nomenclature or want a quick topline summary of a receptor try the official database of the IUPHAR Committee on Receptor Nomenclature and Drug Classification. Incorporating detailed pharmacological, functional and pathophysiological information on G Protein-Coupled Receptors, Voltage-Gated Ion Channels, Ligand-Gated Ion Channels and Nuclear Hormone Receptors.
Access to various toxicology databases.
Toxtree some predictive in silico modelling resoruces (spotted by Tim Ritchie)
PubMed more than 20 million citations for biomedical literature from medline, life science journals and on-line books. Citations may include links to full-text content from PubMed central and publisher websites.
UK pubmed central free access to many papers and millions of abstracts Search 24 million+ abstracts and 1.8 million + full text research articles from PubMed and PubMed Central.
European Patent Office Resource