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Section 10 Index

John Overington's Alignment Database


The database shown here is a tabular representation of a Structural Alignment Database developed by John Overington with colleagues whilst at Birkbeck College, and which he has continued to maintain and develop since joining Pfizer at Sandwich, UK. In reality, it consists of sets of aligned homologous well-resolved structures of proteins or domains of proteins.

The Alignment Database was conceived as the first step in a thorough-going analysis of the dependence of amino-acid substitutions as a function of their structural environment, and to assist in the knowledge-based derivation of `Principles of Protein Structure'. The results of some of that analytical work were published in Protein Science, with a supplementary kinemage.

The set of superposed structures is not made available here, but rather we provide links into our copy of the Brookhaven database, which is a little out of date. The structures are served using chemical/MIME so that your local molecular viewer (eg RasMol) will be automagically invoked, if it is correctly installed and configured, which we strongly recommend. However, bear in mind that we don't have all the structures, and furthermore, the raw PDB files may involve more than the domain alluded to, may be an NMR structure with 16 copies, or may contain only C-alpha atoms.

The tables presented here group known protein structures for which homologues are available into major classes by secondary structure, and then by separate fold types. The entries include additional information on species of origin, as well as the following:-

Column. . . Item

  1. 4-letter PDB code (if beinning with an X - not submitted); followed by five hyperlinks to chemical-MIME version of PDB file; click here for further information
  2. Starting residue
  3. its Chain identifier
  4. Ending residue
  5. its Chain identifier
  6. Protein or domain name
  7. species
  8. nominal resolution (Ângstroms)
  9. percentage sequence ID for set members

am - 12th.Apr'95

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Section 10 Index

Last updated 7th April '97