FATCAT: a web server for flexible structure comparison and structure similarity searching

Protein structure comparison, an important problem in structural biology, has two main applications: (i) comparing two protein structures in order to identify the similarities and differences between them, and (ii) searching for structures similar to a query structure. Many web-based resources for both applications are available, but all are based on rigid structural alignment algorithms. FATCAT server implements the recently developed flexible protein structure comparison algorithm FATCAT, which automatically identifies hinges and internal rearrangements in two protein structures. The server provides access to two algorithms: FATCAT-pairwise for pairwise flexible structure comparison and FATCAT-search for database searching for structurally similar proteins. Given two protein structures [in the Protein Data Bank (PDB) format], FATCAT-pairwise reports their structural alignment and the corresponding statistical significance of the similarity measured as a P-value. Users can view the superposition of the structures online in web browsers that support the Chime plug-in, or download the superimposed structures in PDB format. In FATCAT-search, users provide one query structure and the server returns a list of protein structures that are similar to the query, ordered by the P-values. In addition, FATCAT server can report the conformational changes of the query structure as compared to other proteins in the structure database. FATCAT server is available at http://fatcat.burnham.org.

[1]  J. Séquaris,et al.  Principles of Protein , 1980 .

[2]  H. Wolfson,et al.  Flexible protein alignment and hinge detection , 2002, Proteins.

[3]  J F Gibrat,et al.  Surprising similarities in structure comparison. , 1996, Current opinion in structural biology.

[4]  S. Wodak,et al.  Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteins. , 1995, Protein engineering.

[5]  Adam Godzik,et al.  Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[6]  William R. Taylor,et al.  Structure Comparison and Structure Patterns , 2000, J. Comput. Biol..

[7]  S. Bryant,et al.  Threading a database of protein cores , 1995, Proteins.

[8]  Adam Godzik,et al.  Flexible structure alignment by chaining aligned fragment pairs allowing twists , 2003, ECCB.

[9]  D. Jacobs,et al.  Protein flexibility predictions using graph theory , 2001, Proteins.

[10]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[11]  P E Bourne,et al.  Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. , 1998, Protein engineering.

[12]  Adam Godzik,et al.  Database searching by flexible protein structure alignment , 2004, Protein science : a publication of the Protein Society.

[13]  C. Sander,et al.  Protein structure comparison by alignment of distance matrices. , 1993, Journal of molecular biology.

[14]  Liisa Holm.  Protein structure comparison , 2005 .

[15]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[16]  Georg E. Schulz,et al.  Principles of Protein Structure , 1979 .

[17]  W. Bennett,et al.  Structural and functional aspects of domain motions in proteins. , 1984, CRC critical reviews in biochemistry.

[18]  Chris Sander,et al.  Completeness in structural genomics , 2001, Nature Structural Biology.