Algorithms for optimal protein structure alignment

Bioinformatics

Volumn 25, Issue 21, 2009, Pages 2751-2756

  Poleksic, Aleksandar ^a  

^a UNIVERSITY OF NORTHERN IOWA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; GENETIC CONSERVATION; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; PATTERN RECOGNITION, AUTOMATED; PROTEIN CONFORMATION; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 70350682039     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp530     Document Type: Article

References (35)

1. Andreeva,A. et al. (2007) SISYPHUS - structural alignments for proteins with non-trivial relationships. Nucleic Acids Res., 35 D253-D259.
2. Alexandrov,N.N. et al. (1992) Common spatial arrangements of backbone fragments in homologous and nonhomologous proteins. J. Mol. Biol., 225, 5-9.
3. Caprara,A. et al. (2004) 1001 optimal PDB structure alignments: integer programming methods for finding the maximumcontact map overlap. J. Comput. Biol., 11, 27-52.
4. Csaba,G. et al. (2008) Protein structure alignment considering phenotypic plasticity. Bioinformatics, 24, i98-i104.
5. Eidhammer,I. et al. (2000) Structure comparison and structure patterns. J. Comput. Biol., 7, 685-716.
6. Fischer,D. et al. (2003) CAFASP3: The third critical assessment of fully automated structure prediction methods. Proteins, 53 (Suppl. 6), 503-516.
7. Ginalski,K. et al. (2005) Practical lessons from protein structure prediction. Nucleic Acids Res., 33, 18740-1891.
8. Goldman,D. et al. (1999) Algorithmic aspects of protein structure similarity. In Proceedings of the 40th Annual Symposium on Foundations of Computer Science, IEEE Computer Science, Washington, DC, USA, pp. 512-522.
9. Goldsmith-Fischman,S. and Honig,B. (2003) Structural genomics: computational methods for structure analysis. Prot. Sci., 12 1813-1821.
10. Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
11. Hao,M.H. et al. (1992) Effects of compact volume and chain stiffness on the conformations of native proteins. Proc. Natl Acad. Sci. USA, 89, 6614-6618.
12. Holm,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
13. Kabsch,W. (1976) solution for the best rotation to relate two sets of vectors. Acta Crystallographica, 32, 922-923.
14. Kolodny,R. and Linial,N. (2003) Approximate protein structural alignment in polynomial time. Proc. Natl Acad. Sci. USA, 101, 12201-12206.
15. Konagurthu,A.S. et al. (2006) MUSTANG: Multiple structural alignment algorithm. Proteins, 64, 559-574.
16. Lathrop,R.H. (1994) The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng., 7 1059-1068.
17. Menke,M. et al. (2008) Matt: Local flexibility aids protein multiple structure alignment. PLOS Computat. Biol., 4, 88-99.
18. Moult,J. et al. (2007) Critical assessment of methods of protein structure prediction Round VII. Proteins, 69, 3-9.
19. Murzin,A.G. et al. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
20. Oldfield,T.J. (2007) CAALIGN: A program for pairwise and multiple protein structure alignment. Acta Crystallogr. D Biol. Crystallogr. 63, 514-525.
21. Orengo,C.A. and Taylor,W.R. (1996) SSAP: Sequential structure alignment program for protein structure comparison. Methods Enzymol., 266 617-635.
22. Ortiz,A.R. et al. (2002) MAMMOTH (matching molecular models obtained from theory): An automated method for model comparison. Protein Sci., 11, 2606-2621.
23. Rocha,J. et al. (2009) Flexible structural protein alignment by a sequence of local transformations. Bioinformatics. 25, 1625-1631.
24. Russell,R.B. and Barton,G.J. (1992) Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels. Proteins, 14, 309-323.
25. Sali,A. and Blundell,T.L. (1993) Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
26. Shindyalov,I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
27. Siew,N. et al. (2000) MaxSub: An automated measure for the assessment of protein structure prediction quality. Bioinformatics 16, 776-785.
28. Smith,T.F. and Waterman,M.S. (1981) Identification of Common Molecular Subsequences. J. Mol. Biol., 147, 195-197.
29. Subbiah,S. et al. (1993) Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core. Curr. Biol. 3, 141-148.
30. Taylor,W.R. and Orengo,C.A. (1989) Protein structure alignment. J. Mol. Biol., 208, 1-22.
31. Vriend,G. and Sander,C. (1991) Detection of common three-dimensional substructures in proteins. Proteins, 11, 52-58.
32. Xu,J. et al. (2007) A parameterized algorithm for protein structure alignment. J. Comput. Biol., 14, 564-577.
33. Ye,Y. and Godzik,A. (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics, 19 (Suppl. 2), ii246-ii255.
34. Zemla,A. (2003) LGA - a method for finding 3D similarities in protein structures. Nucleic Acids Res., 31, 3370-3374.
35. Zhang,Y. and Skolnick,J. (2005) TM-align: A protein structure alignment algorithm based on the TM-score. Nucleic Acids Res., 33, 2302-2309.