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This article is part of the supplement: Italian Society of Bioinformatics (BITS): Annual Meeting 2005

Open Access Research article

Query3d: a new method for high-throughput analysis of functional residues in protein structures

Gabriele Ausiello*, Allegra Via and Manuela Helmer-Citterich

Author Affiliations

Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy

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BMC Bioinformatics 2005, 6(Suppl 4):S5  doi:10.1186/1471-2105-6-S4-S5

Published: 1 December 2005



The identification of local similarities between two protein structures can provide clues of a common function. Many different methods exist for searching for similar subsets of residues in proteins of known structure. However, the lack of functional and structural information on single residues, together with the low level of integration of this information in comparison methods, is a limitation that prevents these methods from being fully exploited in high-throughput analyses.


Here we describe Query3d, a program that is both a structural DBMS (Database Management System) and a local comparison method. The method conserves a copy of all the residues of the Protein Data Bank annotated with a variety of functional and structural information. New annotations can be easily added from a variety of methods and known databases. The algorithm makes it possible to create complex queries based on the residues' function and then to compare only subsets of the selected residues. Functional information is also essential to speed up the comparison and the analysis of the results.


With Query3d, users can easily obtain statistics on how many and which residues share certain properties in all proteins of known structure. At the same time, the method also finds their structural neighbours in the whole PDB. Programs and data can be accessed through the PdbFun web interface.