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Nucleic Acids Research Advance Access originally published online on October 30, 2008
Nucleic Acids Research 2009 37(Database issue):D224-D228; doi:10.1093/nar/gkn833
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Nucleic Acids Research, 2009, Vol. 37, Database issue D224-D228
© 2008 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.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

Protein segment finder: an online search engine for segment motifs in the PDB

Abraham O. Samson* and Michael Levitt

Department of Structural Biology, Stanford University, Stanford, CA 94305, USA

*To whom correspondence should be addressed. Tel: +1 650 725 0754; Fax: +1 650 723 8464; Email: avraham.samson{at}stanford.edu

Received August 15, 2008. Revised October 10, 2008. Accepted October 14, 2008.

Finding related conformations in the Protein Data Bank (PDB) is essential in many areas of bioscience. To assist this task, we designed a search engine that uses a compact database to quickly identify protein segments obeying a set of primary, secondary and tertiary structure constraints. The database contains information such as amino acid sequence, secondary structure, disulfide bonds, hydrogen bonds and atoms in contact as calculated from all protein structures in the PDB. The search engine parses the database and returns hits that match the queried parameters. The conformation search engine, which is notable for its high speed and interactive feedback, is expected to assist scientists in discovering conformation homologs and predicting protein structure. The engine is publicly available at http://ari.stanford.edu/psf and it will also be used in-house in an automatic mode aimed at discovering new protein motifs.


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