A fast indexing approach for protein structure comparison

BMC Bioinformatics

Volumn 11, Issue SUPPLL.1, 2010, Pages

  Zhang, Lei ^a   Bailey, James ^a   Konagurthu, Arun S ^a   Ramamohanarao, Kotagiri ^a  

^a UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

EXPERIMENTAL ANALYSIS; INDEXING TECHNIQUES; LARGE-SCALE PROCESSING; ORDERS OF MAGNITUDE; PROTEIN COMPARISON; PROTEIN STRUCTURE COMPARISON; PROTEIN STRUCTURE DATABASE; PROTEIN TERTIARY STRUCTURES;

DATABASE SYSTEMS; INDEXING (OF INFORMATION); INFORMATION RETRIEVAL; BIOINFORMATICS;

PROTEINS;

PROTEIN;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; PROTEIN DATABASE; PROTEIN FOLDING;

ALGORITHMS; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEINS;

EID: 75149131051     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S1-S46     Document Type: Article

References (30)

1. Lesk A. Bioinformatics 2002, Oxford University Press.
2. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, et al. The Protein Data Bank. Acta Crystallographica. Section D, Biological Crystallography 2002, 58(Pt 6 No 1):899-907. 10.1107/S0907444902003451, 12037327.
3. Holm L, Sander C. Mapping the protein universe. Science (New York, NY) 1996, 273(5275):595-603. [PMID: 8662544]..
4. Orengo CA, Taylor WR. SSAP: sequential structure alignment program for protein structure comparison. Methods in Enzymology 1996, 266:617-635. full_text, 8743709.
5. Konagurthu AS, Whisstock JC, Stuckey PJ, Lesk AM. MUSTANG: A multiple structural alignment algorithm. Proteins: Structure, Function, and Bioinformatics 2006, 64(3):559-574.
6. Carugo O, Pongor S. Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison. Journal of Molecular Biology 2002, 315(4):887-898. [PMID: 11812155]., 10.1006/jmbi.2001.5250, 11812155.
7. Kirillova S, Carugo O. Progress in the PRIDE technique for rapidly comparing protein three-dimensional structures. BMC Research Notes 2008, 1:44. [PMC2535597]., 10.1186/1756-0500-1-44, 2535597, 18710497.
8. Lo W, Huang P, Chang C, Lyu P. Protein structural similarity search by Ramachandran codes. BMC Bioinformatics 2007, 8:307. 10.1186/1471-2105-8-307, 2194796, 17716377.
9. Lo W, Lyu P. CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships. Genome Biology 2008, 9:R11. 10.1186/gb-2008-9-1-r11, 2395249, 18201387.
10. Lo W, Lee C, Lee C, Lyu P. iSARST: an integrated SARST web server for rapid protein structural similarity searches. Nucl Acids Res 2009, 37(suppl 2):W545-551. 10.1093/nar/gkp291, 2703971, 19420060., http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_2/W545
11. Carpentier M, Brouillet S, Pothier J. YAKUSA: A fast structural database scanning method. Proteins: Structure, Function, and Bioinformatics 2005, 61:137-151.
12. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. Journal of Molecular Biology 1990, 215(3):403-410. [PMID: 2231712]..
13. Shih ES, Hwang M. Protein structure comparison by probability-based matching of secondary structure elements. Bioinformatics 2003, 19(6):735-741. 10.1093/bioinformatics/btg058, 12691985.
14. Shih ES, Hwang M. Alternative alignments from comparison of protein structures. Proteins: Structure, Function, and Bioinformatics 2004, 56(3):519-527., http://dx.doi.org/10.1002/prot.20124
15. Konagurthu AS, Stuckey PJ, Lesk AM. Structural Search and Retrieval using a Tableau Representation of Protein Folding Patterns. Bioinformatics 2008, 24(5):645-651. 10.1093/bioinformatics/btm641, 18175768.
16. Stivala A, Wirth A, Stuckey P. Tableau-based protein substructure search using quadratic programming. BMC Bioinformatics 2009, 10:153. 10.1186/1471-2105-10-153, 2705363, 19450287.
17. Michalopoulos I, Torrance GM, Gilbert DR, Westhead DR. TOPS: an enhanced database of protein structural topology. Nucl Acids Res 2004, 32:251-254.
18. Krissinel E, Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallographica. Section D, Biological Crystallography 2004, 60(Pt 12 Pt 1):2256-2268. [PMID: 15572779]., 10.1107/S0907444904026460, 15572779.
19. Shapiro J, Brutlag D. FoldMiner: Structural motif discovery using an improved superposition algorithm. Protein Science: A Publication of the Protein Society 2004, 13:278-294. 2286532, 14691242.
20. Richards FM, Kundrot CE. Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure. Proteins 1988, 3(2):71-84. [PMID: 3399495]., 10.1002/prot.340030202, 3399495.
21. Gibrat JF, Madej T, Bryant SH. Surprising similarities in structure comparison. Current Opinion in Structural Biology 1996, 6(3):377-385. 10.1016/S0959-440X(96)80058-3, 8804824.
22. Madej T, Gibrat JF, Bryant SH. Threading a database of protein cores. Proteins 1995, 23(3):356-369. 10.1002/prot.340230309, 8710828.
23. Shih ESC, chi R, Gan R, Hwang M. OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures. Nucl Acids Res 2006, 34(suppl 2):W95-98. 10.1093/nar/gkl264, 1538888, 16845117.
24. Lesk AM. Systematic representation of protein folding patterns. Journal of Molecular Graphics 1995, 13(3):159-164. 10.1016/0263-7855(95)00037-7, 7577843.
25. Kamat AP, Lesk AM. Contact patterns between helices and strands of sheet define protein folding patterns. Proteins: Structure, Function, and Bioinformatics 2007, 66(4):869-876.
26. Tversky A. Features of Similarity. Psychological Review 1977, 84(4):327-352.
27. Jaccard P. Étude comparative de la distribution orale dans une portion des Alpes et des Jura. Bulletin del la Société Vaudoise des Sciences Naturelles 1901, 37:547-579.
28. Brenner SE, Koehl P, Levitt M. The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Research 2000, 28:254-256. 10.1093/nar/28.1.254, 102434, 10592239.
29. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology 1995, 247(4):536-540.
30. Delano WL. The PyMOL Molecular Graphics System. 2002, Palo Alto, CA, USA.