GOSSIP: A method for fast and accurate global alignment of protein structures

Bioinformatics

Volumn 27, Issue 7, 2011, Pages 925-932

  Kifer, I ^a   Nussinov, R ^a   Wolfson, H J ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARTICLE; CHEMISTRY; CLUSTER ANALYSIS; COMPUTER PROGRAM; EVALUATION; PROTEIN DATABASE; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY;

CLUSTER ANALYSIS; DATABASES, PROTEIN; PROTEINS; SEQUENCE ALIGNMENT; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 79953300931     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr044     Document Type: Article

References (37)

1. Alireza,S. et al. (2005) Pads: protein structure alignment using directional shape signatures. Lect. Notes Comput. Sci., 3453.
2. Altschul,S. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
3. Andreeva,A. et al. (2008) Data growth and its impact on the scop database: new developments. Nucleic Acids Res., 36, D419-D425.
4. Baeten,L. et al. (2008) Reconstruction of protein backbones from the brix collection of canonical protein fragments. PLos Comput. Biol., 4.
5. Brenner,S. et al. (2000) The astral compendium for protein structure and sequence analysis. Nucleic Acids Res., 28, 254-256.
6. Bryson,K. et al. (2005) Prediction of novel and analogous folds using fragment assembly and fold recognition. Proteins, 61, 143-151.
7. Budowski-Tal,I. et al. (2010) Fragbag, an accurate representation of protein structure, retrieves structural neighbors from the entire pdb quickly and accurately. Proc. Natl Acad. Sci. USA, 107, 3481-3486.
8. Can,T. and Wang,Y. (2003) Ctss: a robust and efficient method for protein structure alignment based on local geometrical and biological features. IEEE Computer Society Bioinformatics Conf., 2, 169-179.
9. Carpentier,M. et al. (2005)Yakusa: a fast structural database scanning method. Proteins, 61, 137-151.
10. Carugo,O. and Pongor,S. (2002) Protein fold similarity estimated by a probabilistic approach based on c(alpha)-c(alpha) distance comparison. J. Mol. Biol., 315, 887-898.
11. Choi,I. et al. (2004) Local feature frequency profile: a method to measure structural similarity in proteins. Proc. Natl Acad. Sci. USA, 101, 3797-3802.
12. Csaba,G. et al. (2008) Protein structure alignment considering phenotypic plasticity. Bioinformatics, 24, i98-i104.
13. Dror,O. et al. (2003) MASS: multiple structural alignment by secondary structures. Bioinformatics, 19 (Suppl. 1), i95-i104.
14. Friedberg,I. et al. (2007) Using an alignment of fragment strings for comparing protein structures. Bioinformatics, 23, e219-e224.
15. Greene,L. et al. (2007) The cath domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res., 35, D291-D297.
16. Hasegawa,H. and Holm,L. (2009) Advances and pitfalls of protein structural alignment. Curr. Opin. Struct. Biol., 19, 341-348.
17. Holm,L. and Park,J. (2000) Dalilite workbench for protein structure comparison. Bioinformatics, 16, 566-567.
18. Kishon,E. et al. (1991) 3-d curve matching using splines. J. Robot. Syst., 8, 723-743.
19. Kolodny,R. et al. (2005) Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J. Mol. Biol., 346, 1173-1188.
20. Kosloff,M. and Kolodny,R. (2008) Sequence-similar, structure-dissimilar protein pairs in the pdb. Proteins, 71, 891-902.
21. Krissinel,E. and Henrick,K. (2004) Secondary-structure matching (ssm), a new tool for fast protein structure alignment in three dimensions. Acta crystallographica, 60, 2256-2268.
22. Lamdan,Y. and Wolfson,H. (1988) Geomtric hashing: a general and efficient modelbased recognition scheme. Proceedings of the 2nd International Conference on Computer Vision (ICCV). pp. 238-249.
23. Landau,G. et al. (1985) An efficient string matching algorithm with k differences for nucleotide and amino acid sequences. NAR, 14, 31-46.
24. Lisewski,A. and Lichtarge,O. (2006) Rapid detection of similarity in protein structure and function through contact metric distances. Nucleic Acids Res., 34, e152.
25. Needleman,S. and Wunsch,C. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
26. Nussinov,R. and Wolfson,H. (1991). Efficient detection of three-dimensional motifs in biological macromolecules by computer vision techniques. Proc. Natl Acad. Sci. USA, 88, 10495-10499.
27. Orengo,C. et al. (1997) CATH - a hierarchic classification of protein domain structure. Structure, 5, 1093-1108.
28. Pandini,A. et al. (2010) Structural alphabets derived from attractors in conformational space. BMC Bioinformatics, 11, 97.
29. Pearson,W.R. and Lipman,D.J. (1988) Improved tools for biological sequence analysis. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
30. Røgen,P. and Fain,B. (2003) Automatic classification of protein structure by using gauss integrals. Proc. Natl Acad. Sci. USA, 100, 119-124.
31. Shatsky,M. et al. (2004) A method for simultaneous alignment of multiple protein structures. Proteins, 56, 143-156.
32. Shindyalov,I. and Bourne,P. (1998) Protein structure alignment by incremental combinatorical extension (ce) of the optimal path. Protein Eng., 11, 739-747.
33. Subbiah,S. et al. (1993) Structural similarity of dna-binding domains of bacteriophage repressors and the globin core. Curr. Biol., 11, 141-148.
34. Wang,G. and Dunbrack, R.L. (2003) Pisces: a protein sequence culling server. Bioinformatics, 19, 1589-1591.
35. Zhang,Y. and Skolnick,J. (2005a) The protein structure prediction problem could be solved using the current pdb library. Proc. Natl Acad. Sci. USA, 102, 1029-1034.
36. Zhang,Y. and Skolnick,J. (2005b) Tm-align: a protein structure alignment algorithm based on tm-score. Nucleic Acids Res., 33, 2302-2309.
37. Zotenko,E. et al. (2006) Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification. BMC Struct. Biol., 6.