PAR-3D-BLAST: A parallel tool for searching and aligning protein structures

Concurrency and Computation: Practice and Experience

Volumn 26, Issue 10, 2014, Pages 1705-1714

  Salah, Ahmad ^a,b   Li, Kenli ^a  

^a HUNAN UNIVERSITY   (China)

^b Zagazig University   (Egypt)

Author keywords

multi core; parallel algorithm; protein structure; structure alignment; structure searching

Indexed keywords

BIOINFORMATICS; CLASSIFICATION (OF INFORMATION); CLUSTER COMPUTING; DATABASE SYSTEMS; PARALLEL ALGORITHMS; PROTEINS;

DATABASE CONSTRUCTION; EVOLUTIONARY RELATIONSHIPS; MULTI CORE; PROTEIN STRUCTURE COMPARISON; PROTEIN STRUCTURES; STRUCTURAL CLASSIFICATION; STRUCTURAL SIMILARITY; STRUCTURE ALIGNMENT;

QUERY PROCESSING;

EID: 84902553693     PISSN: 15320626     EISSN: 15320634     Source Type: Journal    
DOI: 10.1002/cpe.3114     Document Type: Conference Paper

References (27)

1. Rossmann MG, Patrick A,. The taxonomy of binding sites in proteins. Molecular and Cellular Biochemistry 1978; 21 (3): 161-182.
2. Zhang C, Lai L,. Towards structure-based protein drug design. Biochemical Society Transactions 2011; 39 (5): 1382-1386.
3. Orengo CA, Sillitoe I, Reeves G, Pearl FMG,. Review: what can structural classifications reveal about protein evolution? Journal of Structural Biology 2001; 134 (2): 145-165.
4. Thomas S, Tanase G, Dale LK, Moreira JM, Rauchwerger L, Amato NM,. Parallel protein folding with STAPL. Concurrency and Computation: Practice and Experience 2005; 17 (14): 1643-1656.
5. Hegyi H, Gerstein M,. The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. Journal of Molecular Biology 1999; 288 (1): 147-164.
6. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE,. The protein data bank. Nucleic Acids Research 2000; 28 (1): 235-242.
7. Conte LL, Ailey B, Hubbard TJ, Brenner SE, Murzin AG, Chothia C,. SCOP: a structural classification of proteins database. Nucleic Acids Research 2000; 28 (1): 257-259.
8. Orengo CA, Pearl FM, Thornton JM,. The CATH domain structure database. Structural Bioinformatics 2005; 44: 249-271.
9. Gherardini PF, Helmer-Citterich M,. Structure-based function prediction: approaches and applications. Briefings in Functional Genomics & Proteomics 2008; 7 (4): 291-302.
10. Liu W, Srivastava A, Zhang J,. A mathematical framework for protein structure comparison. PLoS Computational Biology 2011; 7 (2): e1001075.
11. 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 (12): 2256-2268.
12. Harrison A, Pearl F, Sillitoe I, Slidel T, Mott R, Thornton J, Orengo C,. Recognizing the fold of a protein structure. Bioinformatics 2003; 19 (14): 1748-1759.
13. Madej T, Gibrat JF, Bryant SH,. Threading a database of protein cores. Proteins: Structure, Function, and Bioinformatics 2004; 23 (3): 356-369.
14. Holm L, Kääriäinen S, Rosenström P, Schenkel A,. Searching protein structure databases with DaliLite v. 3. Bioinformatics 2008; 24 (23): 2780-2781.
15. Gao F, Zaki MJ,. PSIST: A scalable approach to indexing protein structures using suffix trees. Journal of Parallel and Distributed Computing 2008; 68 (1): 54-63.
16. Gharib TF, Salah A, Salem ABM,. PSISA: an algorithm for indexing and searching protein structure using suffix arrays. Proceedings of the 12th WSEAS International Conference on Computers, Heraklion, Greece, 2008; 775-780.
17. Holm L, Sander C,. Protein structure comparison by alignment of distance matrices. Journal of Molecular Biology 1993; 233 (1): 123-138.
18. Shindyalov IN, Bourne PE,. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering 1998; 11 (9): 739-747.
19. Orengo CA, Taylor WR,. SSAP: sequential structure alignment program for protein structure comparison. Methods in Enzymology 1996; 266: 617-635.
20. Ukkonen E,. On-line construction of suffix trees. Algorithmica 1995; 14 (3): 249-260.
21. Ortiz AR, Strauss CE, Olmea O,. MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Science 2009; 11 (11): 2606-2621.
22. Bonnel N, Marteau PF,. LNA: Fast protein structural comparison using a Laplacian characterization of tertiary structure. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2012; 9 (5): 1451-1458.
23. Braberg H, Webb BM, Tjioe E, Pieper U, Sali A, Madhusudhan MS,. SALIGN: a web server for alignment of multiple protein sequences and structures. Bioinformatics 2012; 28 (15): 2072-2073.
24. Yang JM, Tung CH,. Protein structure database search and evolutionary classification. Nucleic Acids Research 2006; 34 (13): 3646-3659.
25. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ,. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 1997; 25 (17): 3389-3402.
26. Xiangyuan Z, Li K, Salah A,. A data parallel strategy for aligning multiple biological sequences on multi-core computers. Computers in Biology and Medicine 2013; 43 (4): 350-361.
27. Aung Z, Tan KL,. Rapid 3D protein structure database searching using information retrieval techniques. Bioinformatics 2004; 20 (7): 1045-1052.