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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy. ausiello@cbm.bio.uniroma2.it
authors.forename: Gabriele
authors.initials: G
authors.lastname: Ausiello
authors.forename: Allegra
authors.initials: A
authors.lastname: Via
authors.forename: Manuela
authors.initials: M
authors.lastname: Helmer-Citterich
mesh_terms: D000465:Algorithms; D001331:Automation; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030562:Databases, Protein; D008958:Models, Molecular; D015233:Models, Statistical; D015394:Molecular Structure; D011381:Programming Languages; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins