Nucleic Acids Research Advance Access originally published online on May 3, 2007
Nucleic Acids Research 2007 35(Web Server issue):W393-W397; doi:10.1093/nar/gkm236
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W393-W397
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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DBAli tools: mining the protein structure space
1Structural Genomics Unit, 2Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94158-2330, USA and 3Functional Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
*To whom correspondence should be addressed. Tel: +34 96 3289680; Fax: +34 96 3289701; Email: mmarti{at}cipf.es
Received January 30, 2007. Accepted March 31, 2007.
The DBAli tools use a comprehensive set of structural alignments in the DBAli database to leverage the structural information deposited in the Protein Data Bank (PDB). These tools include (i) the DBAlit program that allows users to input the 3D coordinates of a protein structure for comparison by MAMMOTH against all chains in the PDB; (ii) the AnnoLite and AnnoLyze programs that annotate a target structure based on its stored relationships to other structures; (iii) the ModClus program that clusters structures by sequence and structure similarities; (iv) the ModDom program that identifies domains as recurrent structural fragments and (v) an implementation of the COMPARER method in the SALIGN command in MODELLER that creates a multiple structure alignment for a set of related protein structures. Thus, the DBAli tools, which are freely accessible via the World Wide Web at http://salilab.org/DBAli/, allow users to mine the protein structure space by establishing relationships between protein structures and their functions.
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