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PDB-Metrics: a Web tool for exploring the PDB contents
Renato Fileto, Paula R. Kuser, Michel E.B. Yamagishi, André A. Ribeiro,
Thiago G. Quinalia, Eduardo H. Franco, Adauto L. Mancini, Roberto H. Higa,
Stanley R.M. Oliveira, Edgard H. Santos, Fabio D. Vieira, Ivan Mazoni,
Sergio A.B. Cruz and Goran Neshich
Embrapa Information Technology, Campinas, SP, Brasil
Corresponding author: G. Neshich
E-mail: neshich@cbi.cnptia.embrapa.br
Genet. Mol. Res. 5 (2): 333-341 (2006)
Received November 4, 2005
Accepted March 14, 2006
Published June 8, 2006

ABSTRACT. PDB-Metrics (http://sms.cbi.cnptia.embrapa.br/SMS/pdb_metrics/index.html) is a component of the Diamond STING suite of programs for the analysis of protein sequence, structure and function. It summarizes the characteristics of the collection of protein structure descriptions deposited in the Protein Data Bank (PDB) and provides a Web interface to search and browse the PDB, using a variety of alternative criteria. PDB-Metrics is a powerful tool for bioinformaticians to examine the data span in the PDB from several perspectives. Although other Web sites offer some similar resources to explore the PDB contents, PDB-Metrics is among those with the most complete set of such facilities, integrated into a single Web site. This program has been developed using SQLite, a C library that provides all the query facilities of a database management system.

Key words: Protein Data Bank (PDB), PDB data distribution statistics, Search and recovery of the PDB contents

 

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