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Flexible Structural Neighborhood—a database of protein structural similarities and alignments
The Burnham Institute, La Jolla CA, USA
*To whom correspondence should be addressed. Tel: +1 858 646 3168; Fax: +1 858 713 9930; Email: adam{at}burnham.org
Received August 18, 2005. Revised October 20, 2005. Accepted October 20, 2005.
Protein structures are flexible, changing their shapes not only upon substrate binding, but also during evolution as a collective effect of mutations, deletions and insertions. A new generation of protein structure comparison algorithms allows for such flexibility; they go beyond identifying the largest common part between two proteins and find hinge regions and patterns of flexibility in protein families. Here we present a Flexible Structural Neighborhood (FSN), a database of structural neighbors of proteins deposited in PDB as seen by a flexible protein structure alignment program FATCAT, developed previously in our group. The database, searchable by a protein PDB code, provides lists of proteins with statistically significant structural similarity and on lower menu levels provides detailed alignments, interactive superposition of structures and positions of hinges that were identified in the comparison. While superficially similar to other structural protein alignment resources, FSN provides a unique resource to study not only protein structural similarity, but also how protein structures change. FSN is available from a server http://fatcat.burnham.org/fatcat/struct_neighbor and by direct links from the PDB database.
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