PROTEINS

PROTEINS is a program which gives the user access to a local copy of the Protein Data Bank. Structures in the databank are retrieved in a form of files which are capable of being loaded into INTERCHEM.

Features of the program

• For protein structures in the Data Bank the output files may be:-
  • Complete structures
  • Backbone structures
  • Alpha-carbon structures
  • Amino acid sequences (in 3-character format) for use with INTERCHEM and PRESTO
• For nucleic acid and carbohydrate structure only full structure files are retrieved.
• Index of all files reformated from the title and compound records of the databank
• Keyword search of an auxiliary file containing all records except coordinate and connectivity records of the whole databank. Searches may be on (for example) compound names, names of organisms or enzymes, authors names etc.
• Output of files in PDB format for use by other programs.

The program is supplied in a form which assumes that the individual structure files are in compressed form (suffix `code gz), but modification to accomodate the case where the files are in uncompressed form is quite easy. The databank may be held on the users machine or on a different machine on a local area network.

The program is supplied with utility programs to aid in constructing the index and auxiliary keyword files. The index and keyword files are also supplied, but these may not correspond with the latest issue of the databank.

The current version of this program is now available which corresponds with the Release #93 of the Data Bank (July 2000). from the Research Collaboratory for Structural Bioinformatics (RCSB)..

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Revised 18th June 2007