Paper Info
Title
Query3d: a new method for high-throughput analysis of functional residues in protein structures.
Abstract
BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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.
Year
DOI
Venue
2005
10.1186/1471-2105-6-S4-S5
BMC Bioinformatics
Keywords
Field
DocType
protein structure,algorithms,automation,programming languages,molecular structure,web interface,protein data bank,protein folding,computer simulation,sequence alignment,computational biology,database management system,microarrays,bioinformatics,protein conformation,proteins,high throughput
Sequence alignment,Protein folding,High throughput analysis,Computer science,Bioinformatics,Computational biology,DNA microarray,Protein structure
Journal
Volume
Issue
ISSN
6
S-4
1471-2105
Citations 
PageRank 
References 
45
1.12
10
Authors
3
Name
Order
Citations
PageRank
Gabriele Ausiello130123.59
Allegra Via261644.62
Manuela Helmer-Citterich345633.41