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ABSTRACT

Background: The RCSB (Research Collaboratory for Structural Bioinformatics) Protein Data Bank (PDB, www.rcsb.org) is a worldwide repository for 3-D biological macromolecular structure data. A reengineered beta site released in 2004 (pdbbeta.rcsb.org) features improved primary data in new mmCIF and XML formats, results of the Data Uniformity Project. The XML files were obtained using a two-step process: converting PDB to mmCIF, and then converting mmCIF to XML. The conversion software (pdb2cif and mmCIF_loader) is limited to the UNIX platform and not fully automated. To our knowledge, no direct PDB to XML converter is available.

Many biologists still work with files in old PDB format stored in their own collections on local computers and there is still a need for access support. These files are formatted in plain text, organized in 80-character lines, restricted to fixed ranges of character positions defined in the PDB standard, are very long (many over 100 pages), and use abbreviated nametags. Although this format is useful for computer applications, scientists find it time consuming to search for information.

Results: The prototype Universal Research Interchange Format (URI) Software System that we propose allows scientists to convert locally stored PDB files to XML format and then access protein information using user-friendly query interfaces. Our URI PDB-XML Converter component inputs a PDB file and a DTD file (describing the XML model) and outputs a XML file. It also has built-in capability for producing one-letter sequences and calculating phi and psi angles, and including this information in the XML files with the PDB data. Our system features an extensible design to accommodate additional or modified queries, and will accommodate a different DTD. The software is documented and freely available.

Conclusions: The URI PDB-XML Converter is, to our knowledge, the first tool providing direct PDB to XML conversion. It is extensible, and easily modifiable to handle changes in format and XML schema. The URI software is designed to handle the addition of queries as needed and can be easily integrated with other software supporting a web interface, compiled or ad hoc queries, and a mapping from the XML file to a DBMS.

File Name:	File Size:	Description:
*GENERAL PROJECT DOCUMENTATION:*
Paper-2005-08-28-BIOMED.doc	1047 KB	Project Manuscript ( Version dated 8/28/2005)
*PDB-XML CONVERTER - RELATED FILES*
URI_DTD.dtd	40 KB	DTD (Document Type Definition) for our URI XML format.
URI_PDB2XML.pl	284KB	URI PDB to XML Converter
pdb_dtd_table.pm	52 KB	Converter Perl module defining the correspondence between the PDB record names and the DTD element names.
URI-PDB-XML-Converter-Manual.doc	43 KB	User Manual for the URI PDB to XML Converter
pdb1mcp.ent pdb12e8.ent	293 KB 626 KB	two full PDB files to test for the one-letter sequence function of the converter
pdb1mcp.xml	2778 KB	XML file produced by converting the pdb1mcp.ent file
pdb12e8.xml	5146 KB	XML file produced by converting the pdb12e8.ent file
*PDB DATA QUERY - RELATED FILES*
1mcp_dtd_inter.xml	68 KB	Manually created XML file based on the initial DTD design ( URI_DTD_0.dtd - 46 KB). This was created before the design and implementation of the PDB to XML Converter program was finished, and it was used for the design of the URI-PDB
GUI.zip	1108 KB	Archive containing a total 38 files (the GUI queries using XML, XSL, HTML), structured in 20 folders (parent folder named “Demo”); See the main document's Future Work section for more details.
NewDatabaseDesign-07-07-04.zip	699 KB	Archive containing Database and database related files) (694 KB). Just as in the case of the XML queries mentioned above, the database is just a prototype reflecting an older DTD design, and containing an incomplete set of data from the 1MCP PDB file, the same that was manually entered into 1mcp_dtd_inter.xml . See the main document's Future Work section for more details.