Matt: Local flexibility aids protein multiple structure alignment

PLoS Computational Biology

Volumn 4, Issue 1, 2008, Pages 0088-0099

  Menke, Matthew ^a   Berger, Bonnie ^a,b   Cowen, Lenore ^c  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c Tufts University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT; BENCHMARKING; DYNAMIC PROGRAMMING; INVERSE PROBLEMS;

BENCHMARK DATASETS; GEOMETRIC FLEXIBILITY; LOCAL FLEXIBILITY; MODEL PROTEINS; MULTIPLE ALIGNMENT; MULTIPLE STRUCTURE ALIGNMENTS; OPTIMAL ALIGNMENTS; PROTEINS STRUCTURES; RIGID BODY TRANSFORMATION; STRUCTURAL FRAGMENTS;

PROTEINS;

ARTICLE; COMPUTER PROGRAM; GEOMETRY; HOMSTRAD PROGRAM; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; MATT PROGRAM; MOLECULAR MODEL; MULTIPLE STRUCTURE ALIGNMENT; NONHUMAN; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SABMARK PROGRAM; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; ALGORITHM; AMINO ACID SEQUENCE; METHODOLOGY; MOLECULAR GENETICS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 38949150854     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0040010     Document Type: Article

References (46)

1. Levitt M, Gerstein M (1998) A unified statistical framework for sequence comparison and structure comparison. Proc Natl Acad Sci U S A 95: 5913-5920.
2. Chothia C, Lesk A (1986) The relation between sequence and structure in proteins. EMBO J 5: 823-826.
3. Rost B (1999) Twilight zone of protein sequence alignments. Protein Eng 12: 85-94.
4. Dunbrack RL (2006) Sequence comparison and protein structure prediction. Curr Opin Struct Biol 16: 274-284.
5. Abagyan RA, Batalov S (1997) Do aligned sequences share the same fold? J Mol Biol 273: 355-368.
6. Edgar R, Batzoglou S (2006) Multiple sequence alignment. Curr Opin Struct Bio 16: 368-373.
7. Whisstock JC, Lesk AM (2003) Prediction of protein function from protein sequence and structure. Q Res Biophys 36: 307-340.
8. Kinch LN, Grishin NV (2002) Evolution of protein structures and functions. Curr Opin Struct Biol 12: 400-408.
9. Grishin NV (2001) Fold change in evolution of protein structures. J Struct Biol 134: 167-185.
10. Irving JA, Whisstock JC, Lesk AM (2001) Protein structural alignments and functional genomics. Proteins 42: 378-382.
11. Panchenko A, Marchler-Bauer A, Bryant SH (1999) Threading with explicit models for evolutionary conservation of structure and sequence. Proteins (Supplement 3): 133-140.
12. O'Sullivan O, Suhre K, Abergel C, Higgins D, Notredame C (2004) 3DCoffee: Combining protein sequences and structures within multiple sequence alignments. J Mol Biol 340: 385-395.
13. Shindyalov I, Bourne P (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 11: 739-747.
14. Ye Y, Godzik A (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics (Supplement 2): II246-II255.
15. Holm L, Park J (2000) DaliLite workbench for protein structure comparison. Bioinformatics 16: 566-567.
16. Nussinov R, Wolfson H (1991) Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc Natl Acad Sci U S A 88: 10495-10499.
17. Dror O, Benyamini H, Nussinov R, Wolfson H (2003) MASS: Multiple structural alignment by secondary structures. Bioinformatics 19: 95-104.
18. Dror O, Benyamini H, Nussinov R, Wolfson H (2003) Multiple structure alignment by secondary structures: Algorithm and applications. Protein Sci 12: 2492-2507.
19. Kolbeck B, May P, Schmidt-Goenner T, Steinke T, Knapp1 EW (2006) Connectivity independent protein-structure alignment: A hierarchical approach. BMC Bioinformatics 7: 510.
20. Xu J, Jiao F, Berger B (2007) A parameterized algorithm for protein structure alignment. J Comput Biol 14: 564-577.
21. Yuan X, Bystroff C (2005) Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins. Bioinformatics 21: 1010-1019.
22. Goldman D, Istrail S, Papadimitriou CH (1999) Algorithmic aspects of protein structure similarity. In: Beame P, editor. Proceedings of the 40th Annual Symposium on Foundations of Computer Science. Los Alamitos (California): IEEE Computer Society. pp. 512-522.
23. Wang L, Jiang T (1994) On the complexity of multiple sequence alignment. J Comput Biol 1: 512-522.
24. Kolodny R, Linial N (2004) Approximate protein structural alignment in polynomial time. Proc Natl Acad Sci U S A 101: 12201-12206.
25. Eidhammer I, Jonassen I, Taylor WR (2000) Structure comparison and structure patterns. J Comput Biol 7: 685-716.
26. Kabsh W (1978) A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr A 34: 827-828.
27. Ye Y, Godzik A (2005) Multiple flexible structure alignment using partial order graphs. Bioinformatics 21: 2362-2369.
28. Kolodny R, Koehl P, Levitt M (2005) Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures. J Mol Biol 346: 1173-1188.
29. Jung J, Lee B (2000) Protein structure alignment using environmental profiles. Protein Eng 13: 535-543.
30. Suyama M, Matsuo Y, Nishikawa K (1997) Comparison of protein structures using 3D profile alignment. J Mol Evol 44 (Supplement 1): S163-S173.
31. Bonvin A (2006) Flexible protein-protein docking. Curr Opin Struct Biol 16: 194-200.
32. Echols N, Milburn D, Gerstein M (2003) MolMovDB: Analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res 31: 478-482.
33. Lemmen C, Lengauer T, Klebe G (1998) FlexS: A method for fast flexible ligand superposition. J Medicinal Chem 41: 4502-4520.
34. Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D (2005) Review: Progress in modeling of protein structures and interactions. Science 310: 638-642.
35. Singh R, Berger B (2005) ChainTweak: Sampling from the neighbourhood of a protein conformation. In: Altman R, Jung T, Klein T, Dunker K, Hunter L, editors. Proceedings of the 2005 Pacific Symposium on Biocomputing. London: World Scientific Publishing. pp. 54-65.
36. Shatsky M, Nussinov R, Wolfson H (2002) Flexible protein alignment and hinge detection. Proteins 48: 242-256.
37. Mizuguchi K, Deane C, Blundell TL, Overington J (1998) HOMSTRAD: A database of protein structure alignments for homologous families. Protein Sci 11: 2469-2471.
38. VanWalle I, Lasters I, Wyns L (2005) SABmark - A benchmark for sequence alignment that covers the entire known fold space. Bioinformatics 21: 1267-1268.
39. Barton G, Sternberg M (1987) A strategy for the rapid multiple alignment of protein sequences: Confidence levels from tertiary structure comparisons. J Mol Biol 198: 327-337.
40. Murzin A, Brenner S, Hubbard T, Chothia C (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 297: 536-540.
41. Shatsky M, Nussinov R, Wolfson H (2004) A method for simultaneous alignment of multiple protein structures. Proteins 56: 143-156.
42. Konagurthu A, Whisstock J, Stuckey P, Lesk A (2006) MUSTANG: A multiple structural alignment algorithm. Proteins 64: 559-574.
43. Guex N, Peitsch M (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18: 2714-2723.
44. Gerstein M, Levitt M (1998) Comprehensive assessment of automatic structural alignment against a manual standard, the SCOP classification of proteins. Prot Sci 7: 445-456.
45. Hobohm U, Sander C (1994) Enlarged representative set of protein structures. Protein Science 3: 522-524.
46. Jackins C, Tanimoto S (1983) Quad-trees, Oct-trees, and K-trees: A generalized approach to recursive decomposition of euclidean space. IEEE Trans Pattern Anal Mach Intell 5: 533-539.