Local links

• Pick up a copy of the hetero.pdb collection of hetero-compounds (public domain). This file is now also used by the BioMagResBank in their electronic data-deposition process.

• If you are an academic user, or a commercial user with a license for the X-UTIL package, you may also want to download MOLEMAN (to generate O dictionaries from a PDB file), XPLO2D (to generate X-PLOR/CNS and TNT dictionary files from a PDB file), and CT2HET (to query the collection using a simple connectivity-table file); all these programs are part of the X-UTIL package. For more information, see the home page of the Uppsala Software Factory.

• For more information about hetero-dictionaries, read "Dictionaries for Heteros", a short article that appeared in the CCP4 Newsletter.

• More links related to structural bioinformatics can be found here.

Links outside Uppsala

• R&D Chemicals is a free service that allows to find a chemical by its molecular formula, IUPAC name, common name, CAS number, catalog number, substructure or physical characteristics as well as chemical suppliers. [Added 22 Feb 2007]

• Two databases that are dedicated to lipids are LIPID BANK (here) and LMSD (here). [Added 15 Nov 2006]

• Chemicool is a clickable version of the periodic table with lots of information about the chemical elements (here). [Added 11 Oct 2006]

• ChemDB is a very impressive database maintained at UC Irvine that contains ~4 million compounds and useful search options (here). [Added 26 Jul 2006]

• ZINC is a database maintained at UCSF that contains ~4.6 million compounds in ready-to-dock 3D formats (here). [Added 26 Jul 2006]

• ChemicalRegister.com is an "on-line searchable directory of chemical suppliers enabling buyers to easily source manufacturers for price and capacity of commodity and specialty chemicals by name or CAS registry number. Site includes free magazines, jobs, news and events" (here). [Added 27 Apr 2006]

• PLD is a Protein-Ligand Database with binding and other data (here). [Added 27 Apr 2006]

• PDB-Ligand contains information about ligands bound to biomacromolecules and the make-up of their binding sites (here). [Added 18 Jan 2005]

• Reciprocal Net is a project similar to COD (below). It contains freely accessible coordinates of (at present ~3,000) annotated "small molecules" (here). [Added 7 Oct 2004]

• COD is the Crystallography Open Database. It contains freely accessible coordinates of (at present ~12,000) "small molecules" (here). [Added 7 Oct 2004]

• The RCSB's ligand search tool is called Ligand Depot (here). [Added 14 Nov 2003]

• A small subset of the ICSD (Inorganic Crystal Structure Database) is available on-line to the public (here). [Added 30 Jul 2003]

• You can analyse ligand-protein contacts with the LPC server (here). [Added 3 Jul 2003] [Updated 3 Mar 2006]

• You can search more than 250,000 structures in the NCI database using the enhanced browser of Wolf Ihlenfeldt (here). [Added 20 Jun 2003]

• MolSoft provides a number of interesting free on-line tools: 2D-to-3D (and drawing-to-Smiles) converter (here), small-molecule structure search (here), and a simple PDB viewer (here). [Added 20 Jun 2003]

• Ligand-Info, a Java tool for clustering and retrieval of small molecules [doesn't work on my SGI or Mac, though] (here). [Added 26 May 2003]

• The pitfalls involved in figuring out the chemical structure of a compound from a set of PDB ATOM and HETATM records are described by Roger Sayle (here). [Added 3 Mar 2003]

• Protein-Ligand Database at Cambridge (here). [Added 25 Feb 2003]

• Molecules of the Month (annotated) at Oxford (here). [Added 10 Feb 2003]

• RESID is a database of post-translationally modified amino acids. For every entry a model in PDB format is provided (here). [Added 5 Feb 2003]

• Marjorie Harding maintains a website that contains a range of information on metal sites in metalloproteins containing Ca, Mg, Mn, Fe, Cu, Zn, K and Na (here). [Added 10 Sep 2002]

• A description of the geometry definition in TNT can be found here. [Updated 10 Sep 2002]

• Retrieve information about elements in the periodic table with WebEelements. [Updated 10 Sep 2002]

• ChemNet is a gateway to chemical business worldwide (here). [Updated 10 Sep 2002]

• SWEET is a Web-based facility for quickly generating reasonable 3D coordinates for oligosaccharides. [Updated 10 Sep 2002]

• The IMB Jena Image Library of Biological Macromolecules now includes a Hetero Components Database. [Updated 10 Sep 2002]

• Ftp the PDB dictionary of hetero compounds. [Updated 10 Sep 2002]

• NCI Database. The National Cancer Institute database of over 200,000 molecules, with anti-HIV and anti-cancer assay data is now available free-of-charge. The database is searchable by chemical name, structure, and substructure. Screening assay data is displayed automatically with results. Update: when checked at 10 September 2002, the database was no longer freely accessible, but instead one is rerouted to this site at CambridgeSoft. [Updated 10 Sep 2002]

• Sometimes people use HIC-Up to locate information about a certain compound, and then they send me an E-mail to order it ... I'm sorry, but my organic chemistry is a trifle rusty ! If you want to get a product quotation from a real chemicals supplier, you may want to give ChemACX.Com or ChemStore.Com a try. [Updated 10 Sep 2002]

• Roy Lancaster has developed topology and parameter files for the Rp. viridis RC cofactors (haem c, bacteriochlorophyll b, bacteriopheophytin b, the carotenoid 1,2-dihydroneurosporene, menaquinone, ubiquinone, and a non-haem iron), for use in conjunction with the protein parameters of Engh and Huber (1991). These parameters are based on statistics derived from structures in the Cambridge Structural Database (CSD) and are described in: C Roy D Lancaster and Hartmut Michel (1997). The coupling of light-induced electron transfer and proton uptake as derived from crystal structures of reaction centres from Rhodopseudomonas viridis modified at the binding site of the secondary quinone, QB. Structure 5, 1339-1359. There is also a description of how he calibrated his force constants to those of Engh & Huber. [Updated 10 Sep 2002]

• The CCDC, the Cambridge Crystallographic Data Centre, home of the CSD (the Cambridge Structural Database System). [Updated 10 Sep 2002]

• RELIBase, an archive for structural data about receptor/ligand complexes. [Updated 10 Sep 2002]

• For infrequent academic users of the Cambridge Database (located in continental Europe), there is a free service, offered by the CMBI in the Netherlands. Infrequent academic users in the UK can obtain access through the UK National Chemical Database Service at the Daresbury Laboratory. [Updated 10 Sep 2002]

• The Heavy-Atom Databank, for information about compounds containing heavy atoms used by crystallographers to make derivatives. [Updated 10 Sep 2002]

• The Klotho alphabetical list of small molecules found in PDB files. [Updated 10 Sep 2002]

• Several useful services are provided by the Computer Chemistry Center at the University of Erlangen-Nürnberg. In particular, their CACTVS system may be useful. [Updated 10 Sep 2002]

• LIGBASE (Database of Aligned Ligand Binding Proteins; Rockefeller). [Added 9 Aug 2002]

• The PROMISE site in Leeds contains tons of information about prosthetic groups and metal ions in protein structures. There is a mirror at Scripps. [Updated 9 Aug 2002]

• The PRODRG server in Dundee offers an easy-to-use alternative to the HIC-Up server (here). [Added 6 Aug 2001]

• On the PDBsum site: up-to-date lists of all HET groups and all ligands in the PDB. [Added 18 May 2001]

• NIST WebBook is a gateway to the data collections of the National Institute of Standards and Technology. It can be accessed here. [Added 18 May 2001]

• IUPAC nomenclature information can be accessed here. [Added 1 Dec 2000]

• The SMILES homepage lives here. [Added 1 Dec 2000]

• Have a look at the Periodic Table Hetero Components Element Browser in Jena (here). [Added 9 Nov 1999]

• Through ChemWeb.com (free membership) you can now search the Combined Chemical Dictionary (here). [Added 1 Nov 1999]

• NIST maintains the Chemistry Webbook with lots of information regarding small molecules (here). [Added 18 Oct 1999]

• John Westbrook (Rutgers) is finally doing what somebody ought to have done a long time ago, namely to generate validated dictionaries of hetero-compounds using the CSD. The project is called "A La Mode". [Added 23 Sep 1998]

• The Metalloprotein Group at Scripps maintains MDB, the Metalloprotein Database Browser. [Added 28 Apr 1998]

• Lesa Beamer maintains a site devoted to glycerolipids, containing general information, figures, references and coordinates in PDB format (often not available from other databases). [Updated 28 Apr 1998]

• A very useful facility called ChemFinder is provided by CambridgeSoft. You can search for compounds using different criteria, and if your compound is found, you tend to get a long list of hyperlinks to other sites relevant to this particular compound.

• Will McClure uses the hetero-compound collection in his teaching .

• The 3D Drug Structure Databank at NIH.

• The MathMol Library of small molecule structures, and their page with links to other 3D databases.

• Try the ECTOC Hyperglossary at Imperial College, London.

Please, send additions and corrections to this list to Gerard.