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NAR Molecular Biology Database Collection entry number 818
Li Z., Ye Y. and Godzik A.
The Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA

Database Description

FSN (Flexible Structural Neighborhood) is a database of protein structural similarities and alignments. It employs the flexible protein structure alignment program, FATCAT, to define similarities between all protein structures deposited in the PDB. The FSN interface enables the efficient retrieval of lists of proteins with statistically significant structural similarity to protein or domain queries (via their PDB or SCOP identifiers, respectively). The server also allows users to analyze the identified structural neighbors by providing detailed alignments, interactive superposition of structures and highlighting hinge positions identified by flexible structural comparison. FSN is a unique resource to support the analysis of protein structure, and may prove valuable in unveiling the rules that govern protein change and evolution.

Recent Developments

Jmol view has been added to the standard Chime view of protein structure superposition.


The research was supported by the NSF grant DBI 0349600. We gratefully acknowledge help from our colleagues from the Burnham Bioinformatics group and from PDB for being first beta testers of FSN.


1. Yuzhen Ye and Adam Godzik (2005) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics, 19(Suppl. 2):ii246-ii255.
2. Yuzhen Ye and Adam Godzik (2004) Database searching by flexible protein structure alignment. Protein Sci. 13: 1841-1850
3. Yuzhen Ye and Adam Godzik (2004) FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res., 32(Web Server issue):W582-585.

Subcategory: Protein structure

Go to the abstract in the NAR 2006 Database Issue.
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