deconSTRUCT: General purpose protein database search on the substructure level

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  Zhang, Zong Hong ^a   Bharatham, Kavitha ^a   Sherman, Westley A ^a   Mihalek, Ivana ^a  

^a BIOINFORMATICS INSTITUTE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; INFORMATION PROCESSING; PERFORMANCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SENSITIVITY AND SPECIFICITY; WEB BROWSER; INTERNET; STRUCTURAL HOMOLOGY;

ALGORITHMS; DATABASES, PROTEIN; INTERNET; PROTEIN STRUCTURE, SECONDARY; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN; USER-COMPUTER INTERFACE;

EID: 77954301968     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq489     Document Type: Article

References (34)

1. Madej,T., Gibrat,J. and Bryant,S. (1995) Threading a database of protein cores. Protein Struct. Funct. Genet., 23, 356-369.
2. Krissinel,E. and Henrick,K. (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D, 60, 2256-2268.
3. Holm,L., Kaariainen,S., Rosenstrom,P. and Schenkel,A. (2008) Searching protein structure databases with DaliLite v. 3. Bioinformatics, 24, 2780.
4. Lo,W., Lee,C., Lee,C. and Lyu,P. (2009) iSARST: an integrated SARST web server for rapid protein structural similarity searches. Nucleic Acids Res., 37, W545-W551.
5. Ye,Y. and Godzik,A. (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics, 19(Suppl. 2), 246-255.
6. Margraf,T., Schenk,G. and Torda,A. (2009) The SALAMI protein structure search server. Nucleic Acids Res., 37(Web Server issue), W480.
7. Kolbeck,B., May,P., Schmidt-Goenner,T., Steinke,T. and Knapp,E. (2006) Connectivity independent protein-structure alignment: a hierarchical approach. BMC Bioinformatics, 7, 510.
8. Leslin,C., Abyzov,A. and Ilyin,V. (2007) TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. Nucleic Acids Res., 35(Database issue), D317.
9. Martin,A. (2000) The ups and downs of protein topology; rapid comparison of protein structure. Protein Eng. Design Sel., 13, 829-837.
10. Roegen,P. and Fain,B. (2003) Automatic classification of protein structure by using Gauss integrals. Proc. Natl Acad. Sci. USA, 100, 119-124.
11. Lisewski,A. and Lichtarge,O. (2006) Rapid detection of similarity in protein structure and function through contact metric distances. Nucleic Acids Res., 34, e152.
12. Konagurthu,A., Stuckey,P. and Lesk,A. (2008) Structural search and retrieval using a tableau representation of protein folding patterns. Bioinformatics, 24, 645.
13. Carpentier,M., Brouillet,S. and Pothier,J. (2005) YAKUSA: a fast structural database scanning method. Proteins, 61, 137-151.
14. Shi,S., Chitturi,B. and Grishin,N. (2009) ProSMoS server: a pattern-based search using interaction matrix representation of protein structures. Nucleic Acids Res., 37, W526.
15. Hasegawa,H. and Holm,L. (2009) Advances and pitfalls of protein structural alignment. Curr. Opin. Struct. Biol., 19, 341-348.
16. Teichert,F., Bastolla,U. and Porto,M. (2007) SABERTOOTH: protein structural alignment based on a vectorial structure representation. BMC Bioinformatics, 8, 425.
17. Ortiz,A., Strauss,C. and Olmea,O. (2002) MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci., 11, 2606.
18. Zhang,Y. and Skolnick,J. (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res., 33, 2302.
19. Plewczynski,D., Pas,J., Von Grotthuss,M. and Rychlewski,L. (2002) 3D-Hit, Fast Structural Comparison of Proteins. Appl. Bioinform., 1, 223.
20. Shindyalov,I. and Bourne,P. (1998) Protein structure alignment by incremental combinatorial extension (ce) of the optimal path. Protein Eng., 11, 739-747.
21. Holm,L. and Sander,C. (1995) Dali: a network tool for protein structure comparison. Trends Biochem. Sci., 20, 478-480.
22. Orengo,C. and Taylor,W. (1996) SSAP: sequential structure alignment program for protein structure comparison. Methods Enzymol., 266, 617.
23. Gerstein,M. and Levitt,M. (1998) Comprehensive assessment of automatic structural alignment against a manual standard, the SCOP classification of proteins. Protein Sci., 7, 445.
24. Zhu,J. and Weng,Z. (2005) FAST: a novel protein structure alignment algorithm. Proteins Struct. Funct. Bioinform., 58, 618-627.
25. Mosca,R., Brannetti,B. and Schneider,T. (2008) Alignment of protein structures in the presence of domain motions. BMC Bioinformatics, 9, 352.
26. Sippl,M. (2008) On distance and similarity in fold space. Bioinformatics, 24, 872.
27. Zhang,Z.H., Lee,H.K. and Mihalek,I. (2010) Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity. BMC Bioinformatics, 11, 155.
28. Berman,H., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T., Weissig,H., Shindyalov,I. and Bourne,P. (2000) The protein data bank. Nucletc Acids Res., 28, 235-242.
29. DeLano,W. (2002) The PyMOL Molecular Graphics System, www.pymol.org.
30. Pettersen,E., Goddard,T., Huang,C., Couch,G., Greenblatt,D., Meng,E. and Ferrin,T. (2004) UCSF Chimera visualization system for exploratory research and analysis. J. Comp. Chem., 25, 1605-1612.
31. Jmol: an open-source Java viewer for chemical structures in 3D. www.jmol.org.
32. Frishman,D. and Argos,P. (1995) Knowledge-based protein secondary structure assignment. Proteins Struct. Funct. Genet., 23, 566-579.
33. Sippl,M. and Wiederstein,M. (2008) A note on difficult structure alignment problems. Bioinformatics, 24, 426.
34. Orengo,C., Michie,A., Jones,S., Jones,D., Swindells,M. and Thornton,J. (1997) CATH - a hierarchic classification of protein domain structures. Structure, 5, 1093-1108.