MICAN : A protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, Cα only models, Alternative alignments, and Non-sequential alignments

BMC Bioinformatics

Volumn 14, Issue , 2013, Pages

  Minami, Shintaro ^a   Sawada, Kengo ^a   Chikenji, George ^a  

^a NAGOYA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR PERMUTATION; PHYSICOCHEMICAL PROPERTY; PROTEIN STRUCTURE ALIGNMENT; SECONDARY STRUCTURE ELEMENTS; SECONDARY STRUCTURES; STRUCTURAL ALIGNMENTS; STRUCTURAL RELATIONSHIP; STRUCTURE COMPARISONS;

ALGORITHMS; BENCHMARKING; C (PROGRAMMING LANGUAGE); CHEMICAL PROPERTIES; PHYSICAL CHEMISTRY; PROTEINS;

ALIGNMENT;

PROTEIN;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; EVALUATION; PROTEIN SECONDARY STRUCTURE; STRUCTURAL HOMOLOGY;

ALGORITHMS; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; PROTEINS; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 84872329258     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-24     Document Type: Article

References (51)

1. Matsuo Y, Bryant SH. Identification of homologous core structures. Proteins 1999, 35:70-9. 10.1002/(SICI)1097-0134(19990401)35:1<70::AID-PROT7>3.0.CO;2-9, 10090287.
2. Cheng H, Kim B, Grishin NV. Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets. J Mol Biol 2008, 377(4):1265-78. 10.1016/j.jmb.2007.12.076, 18313074.
3. Szustakowski JD, Kasif S, Weng Z. Less is more: towards an optimal universal description of protein folds. Bioinformatics 2005, 21(Suppl 2):ii66-71. 10.1093/bioinformatics/bti1111, 16204127.
4. Novotny M, Madsen D, Kleywegt GJ. Evaluation of protein fold comparison servers. Proteins 2004, 54(2):260-70.
5. Kolodny R. Inverse Kinematics in Biology: The Protein Loop Closure Problem. Int J Rob Res 2005, 24(2-3):151-163.
6. Mayr G, Domingues FS, Lackner P. Comparative analysis of protein structure alignments. BMC Struct Biol 2007, 7:50. 10.1186/1472-6807-7-50, 1959231, 17672887.
7. Lindqvist Y, Schneider G. Circular permutations of natural protein sequences: structural evidence. Curr Opin Struct Biol 1997, 7(3):422-7. 10.1016/S0959-440X(97)80061-9, 9204286.
8. Jung J, Lee B. Circularly permuted proteins in the protein structure database. Protein Sci 2001, 10(9):1881-1886. 10.1110/ps.05801, 2253204, 11514678.
9. Schmidt-Goenner T, Guerler A, Kolbeck B, Knapp EW. Circular permuted proteins in the universe of protein folds. Proteins 2010, 78(7):1618-30. 10.1002/prot.22678, 20112421.
10. Abyzov A, Ilyin VA. A comprehensive analysis of non-sequential alignments between all protein structures. BMC Struct Biol 2007, 7:78. 10.1186/1472-6807-7-78, 2213659, 18005453.
11. Grishin NV. Fold change in evolution of protein structures. J Struct Biol 2001, 134(2-3):167-85. 10.1006/jsbi.2001.4335, 11551177.
12. Murzin A, Brenner S, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247(4):536-540.
13. Dror O. MASS: multiple structural alignment by secondary structures. Bioinformatics 2003, 19(90001):95i-104.
14. 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):2256-68.
15. Ilyin V, Abyzov A, Leslin C. Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. Protein Sci 2004, 13(7):1865-1874. 10.1110/ps.04672604, 2279929, 15215530.
16. Yuan X, Bystroff C. Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins. Bioinformatics 2005, 21(7):1010-9. 10.1093/bioinformatics/bti128, 15531601.
17. Shih ESC, Gan RR, Hwang M. OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures. Nucleic Acids Res 2006, 34(Web Server issue):W95-8. 1538888, 16845117.
18. Chen L, Wu L, Wang Y, Zhang S, Zhang X. Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison. BMC Struct Biol 2006, 6:18. 10.1186/1472-6807-6-18, 1574323, 16948858.
19. Dundas J, Binkowski TA, DasGupta B, Liang J. Topology independent protein structural alignment. BMC Bioinformatics 2007, 8:388. 10.1186/1471-2105-8-388, 2096629, 17937816.
20. Kolbeck B, May P, Schmidt-Goenner T, Steinke T, Knapp E. Connectivity independent protein-structure alignment: a hierarchical approach. BMC Bioinformatics 2006, 7:510. 10.1186/1471-2105-7-510, 1683948, 17118190.
21. Guerler A, Knapp E. Novel protein folds and their nonsequential structural analogs. Protein Sci 2008, 17(8):1374-1382. 10.1110/ps.035469.108, 2492825, 18583523.
22. Salem S, Zaki M. Iterative non-sequential protein structural alignment. Computational systems bioinformatics 2008, 7(3):183.
23. Cheng H, Kim B, Grishin NV. MALISAM: a database of structurally analogous motifs in proteins. Nucleic Acids Res 2008, 36(Database issue):D211-7. 2238938, 17855399.
24. Kinjo A. Similarity search for local protein structures at atomic resolution by exploiting a database management system. Biophysics 2007, 3:75-84.
25. Kinjo AR, Nakamura H. Comprehensive structural classification of ligand-binding motifs in proteins. Structure 2009, 17(2):234-46. 10.1016/j.str.2008.11.009, 19217394.
26. Nussinov R, Wolfson HJ. Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc National Acad Sci U S A 1991, 88(23):10495-9.
27. Alesker V, Nussinov R, Wolfson HJ. Detection of non-topological motifs in protein structures. Protein Eng 1996, 9(12):1103-19. 10.1093/protein/9.12.1103, 9010924.
28. Kim C, Lee B. Accuracy of structure-based sequence alignment of automatic methods. BMC Bioinformatics 2007, 8:355. 10.1186/1471-2105-8-355, 2039753, 17883866.
29. Teichert F, Bastolla U, Porto M. SABERTOOTH: protein structural alignment based on a vectorial structure representation. BMC Bioinformatics 2007, 8:425. 10.1186/1471-2105-8-425, 2257979, 17974011.
30. Berbalk C, Schwaiger CS, Lackner P. Accuracy analysis of multiple structure alignments. Protein Sci 2009, 18(10):2027-35. 10.1002/pro.213, 2786966, 19621383.
31. Armougom F, Moretti S, Keduas V, Notredame C. The iRMSD: a local measure of sequence alignment accuracy using structural information. Bioinformatics 2006, 22(14):e35-9.
32. Pei J, Kim B, Grishin NV. PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res 2008, 36(7):2295-300. 10.1093/nar/gkn072, 2367709, 18287115.
33. Daniluk P, Lesyng B. A novel method to compare protein structures using local descriptors. BMC Bioinformatics 2011, 12:344. 10.1186/1471-2105-12-344, 3179968, 21849047.
34. Alexandrov NN. SARFing the PDB. Protein Eng 1996, 9(9):727-32. 10.1093/protein/9.9.727, 8888137.
35. Cheng H, Kim B, Grishin NV. MALIDUP: A database of manually constructed structure alignments for duplicated domain pairs. Proteins 2008, 70(4):1162-1166.
36. Holm L, Park J. DaliLite workbench for protein structure comparison. Bioinformatics 2000, 16(6):566-7. 10.1093/bioinformatics/16.6.566, 10980157.
37. Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005, 33(7):2302-9. 10.1093/nar/gki524, 1084323, 15849316.
38. Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998, 11(9):739-47. 10.1093/protein/11.9.739, 9796821.
39. Chothia C, Lesk A. The relation between the divergence of sequence and structure in proteins. EMBO j 1986, 5(4):823-826. 1166865, 3709526.
40. Sierk M, Pearson W. Sensitivity and selectivity in protein structure comparison. Protein Sci 2004, 13(3):773-785. 10.1110/ps.03328504, 2286722, 14978311.
41. Guerler A, Knapp E. GIS: a comprehensive source for protein structure similarities. Nucleic Acids Res 2010, 38(Web Server issue):W46-52. 2896118, 20460464.
42. Xu J, Zhang Y. How significant is a protein structure similarity with TM-score = 0.5?. Bioinformatics 2010, 26(7):889-95. 10.1093/bioinformatics/btq066, 2913670, 20164152.
43. Johnston SC, Larsen CN, Cook WJ, Wilkinson KD, Hill CP. Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 A resolution. EMBO j 1997, 16(13):3787-96. 10.1093/emboj/16.13.3787, 1170002, 9233788.
44. Vivares D, Arnoux P, Pignol D. A papain-like enzyme at work: native and acyl-enzyme intermediate structures in phytochelatin synthesis. Proc National Acad Sci U S A 2005, 102(52):18848-53.
45. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22(12):2577-637. 10.1002/bip.360221211, 6667333.
46. Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995, 23(4):566-79. 10.1002/prot.340230412, 8749853.
47. Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004, 57(4):702-10. 10.1002/prot.20264, 15476259.
48. Andreeva A, Prlić A, Hubbard TJP, Murzin AG. SISYPHUS-structural alignments for proteins with non-trivial relationships. Nucleic Acids Res 2007, 35(Database issue):D253-9. 1635320, 17068077.
49. Stebbings LA, Mizuguchi K. HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database. Nucleic Acids Res 2004, 32(Database issue):D203-7. 308761, 14681395.
50. Hamprecht FA, Scott W, van Gunsteren WF. Generation of pseudonative protein structures for threading. Proteins 1997, 28(4):522-9. 10.1002/(SICI)1097-0134(199708)28:4<522::AID-PROT6>3.0.CO;2-B, 9261868.
51. Taylor WR. Decoy models for protein structure comparison score normalisation. J Mol Biol 2006, 357(2):676-99. 10.1016/j.jmb.2005.12.084, 16457842.