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

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 ...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Gabriele Ausiello, Allegra Via, Manuela Helmer-Citterich
• Keywords: BMCBI 2005, Comparison Methods, Protein, Protein Structures