Abstract
BackgroundThe 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.ResultsHere 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.ConclusionWith 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.
Highlights
The identification of local similarities between two protein structures can provide clues of a common function
Regions of local similarity can be searched between any pair of protein structures, between a protein chain and the whole PDB or between any two arbitrary and chosen subsets of aminoacids in a structure
The second possibility consists in the use of Query3d as a database management system (DBMS) devoted to the functional analysis of protein structures
Summary
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. 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. A lot of information on the relationship between structure and function lies hidden in the high number of known protein structures. Since speed is one of the most treated and fundamental features, some of these methods are able to search accurately a structural motif in the whole set of known structures in a very short time.
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