Search similar protein structures with classification, sequence and 3D alignments

Journal of Bioinformatics and Computational Biology

Volumn 7, Issue 5, 2009, Pages 755-771

  Lu, Zaixin ^a   Zhao, Zhiyu ^b   Garcia, Sergio ^a   Krishnaswamy, Krishnakumar ^a   Fu, Bin ^a  

^a UNIVERSITY OF TEXAS PAN AMERICAN   (United States)

^b USA   (United States)

Author keywords

Protein search; Protein structure alignment

Indexed keywords

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; INTERNET; ONLINE SYSTEM; PROTEIN DATA BANK; PROTEIN DATABASE; PROTEIN STRUCTURE; SEARCH ENGINE; SEQUENCE ALIGNMENT; STRUCTURAL BIOINFORMATICS; STRUCTURAL HOMOLOGY; THREE DIMENSIONAL IMAGING;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, PROTEIN; INTERNET; MODELS, MOLECULAR; PROTEINS; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 70349642680     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S021972000900431X     Document Type: Article

References (36)

1. Altschul S, Gish W, Miller W, Myers E, Lipman D, Basic local alignment search tool, J Mol Biol 3:403-410, 1990.
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman D, Gapped blast and psi-blast: A new generation of protein database search programs, Nucleic Acids Res 17:3389-3402, 1997.
3. Berman H, Westbrook J, Feng Z, The protein data bank, Nucleic Acids Res 28(1): 235-242, 2000.
4. Baker EN, Dauter Z, Secondary-structure matching, a new tool for fast protein structure alignment in three dimensions, Acta Crystallographica 6:2256-2268, 2004.
5. Chew LP, Kedem K, Huttenlocher DP, Kleinberg J, Fast detection of geometric substructure in proteins, J Comput Biol 6:313-325, 1999.
6. Holm L, Sander C, Protein structure comparison by alignment of distance matrices, Journal of Molecular Biology 233:123-138, 1993.
7. Ilyin VA, Abyzov A, Leslin CM, Structural alignment of proteins by a novel topofit method, as a superimposition of common volumes at a topomax point, Protein Science 13:1865-1874, 2004.
8. Lessel U, Schomburg D, Similarities between protein 3D structures, Protein Eng 7(10):1175-1187, 1994.
9. Madej T, Gibrat JF, Bryant SH, Threading a database of protein cores, Proteins 23:356-369, 1995.
10. Shindyalov IN, Bourne PE, Protein structure alignment by incremental combinatorial extension (ce) of the optimal path, Protein Eng 11:739-747, 1998.
11. Singh AP, Brutlag DL, Hierarchical protein superposition using both secondary structure and atomic representation, in Proc Intelligent Systems for Molecular Biology, pp. 284-293, 1997.
12. Ye J, Janardan R, Liu S, Pairwise protein structure alignment based on an orientation-independent backbone representation, J Bioinform Comput Biol 4(2):699-717, 2005.
13. Ye Y, Godzik A, Database searching by flexible protein structure alignment, Protein Science 13(7):1841-1850, 2004.
14. Jiang M, Xu Y, Zhu B, Protein structure-structure alignment with discrete frechet distance, J Bioinform Comput Biol 6 (1):51-64, 2008.
15. Alexandrov NN, Fischer D, Analysis of topological and montopological structural similarities in the pdb: New examples from old structures, Proteins 25:354-365, 1996.
16. Aung Z, Tan KL, Rapid 3D protein structure database searching using information retrieval techniques, Bioinformatics 20 (7):1045-1052, 2004.
17. Camoglu O, Kahveci T, Singh AK, Psi: Indexing protein structures for fast similarity search, in Proceedings of Elventh International Conference on Intelligent Systems for Molecular Biology, pp. 81-83, 2003.
18. Chi P-H, Scott G, Shyu C-R, A fast protein structure retrieval system using image-based distance matrices and multidimensional index, in Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering, pp. 522-532, 2004.
19. Koch I, Lengauer T, Wanke E, An algorithm for finding maximal common subtopolgies in a set of protein structures, J Comput Biol 3 (2):289-306, 1996.
20. Martin ACR, The ups and downs of protein topology; rapid comparison of protein structure, Protein Eng 13:829-837, 2000.
21. Lo W-C, Huang P-J, Chang C-H, Lyu P-C, Protein structrual similarity search by ramachandran codes, BMC Bioinformatics 8:307, 2007.
22. Lu Z, Zhao Z, Garcia S, Fu B, New algorithm and web server for finding proteins with similar 3d structures, In the 2008 International Conference on Bioinformatics & Computational Biology (BIOCOMP'08), pp. 674-680, 2008.
23. Mizguchi K, Go N, Comparison of spatial arrangements of secondary structural elements in proteins, Protein Eng 8:353-362, 1995.
24. Rufino SD, Blundell TL, Structure-based identification and clustering of protein families and superfamilies, J Comput Aided Mol Dec 233 123-138, 1994.
25. Yang J-M, Tung C-H, Protein structure database search and evolutionary classification, Nucleic Acids Res 1:3646-3659, 2006.
26. Hobohm U, Sander C, Enlarged representative set of protein structures, Protein Science 3:522-524, 1994.
27. Holm L, Sander C, The fssp database of structurally aligned protein fold families, Nucleic Acids Res 22:3600-3609, 1994.
28. Mizuguchi K, Deane CM, Blundell TL, Overington JP, Homstrad: A database of protein structure alignments for homologous families, Protein Science 7:2469-2471, 1998.
29. Murzin AG, Brenner SE, Hubbard T, Chothia C, Scop: A structural classification of proteins database for the investigation of sequences and structures, J Mol Biol 247:536-540, 1995.
30. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM, Cath-a hierarchic classification of protein domain structures, Structure 5:1093-1108, 1997.
31. Sander C, Schneider R, Database of homology-derived protein structures and the structural meaning of sequence alignment, in Proc Struct Funct Genet, pp. 56-68, 1991.
32. Zhao Z, Fu B, A flexible algorithm for pairwise protein structure alignment, in Proceedings International Conference on Bioinformatics and Computational Biology 2007, pp. 16-22, 2007.
33. Zhao Z, Fu B, Alanis FJ, Summa CM, Feedback algorithm and web-server for protein structure alignment, J Comput Biol 15(5):505-524, 2008.
34. Kabsch W, Sander C, Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22(12):2577-2637, 1983.
35. Liu W, Mao F, Lai L, Han Y, Protein fold recognition based on structural classification, Acta Biophysica Sinica 15:126-136, 1999.
36. Holm L, Kaariainen S, Rosenstrom P, Schenkel A, Protein structure database searching by Dalilite v. 3, Bioinformatics 24 (23):2780-2781, 2008.