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Volumn 12, Issue 2, 2011, Pages 163-175

Critical assessment of structure-based sequence alignment methods at distant relationships

Author keywords

Distantly related protein domains; Evolutionary divergence; Evolutionary relationships; Protein domain superfamilies; Protein structures

Indexed keywords

PROTEIN;

EID: 79953134243     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbq025     Document Type: Article
Times cited : (10)

References (38)
  • 2
    • 0035783063 scopus 로고    scopus 로고
    • Fold change in evolution of proteins structures
    • Grishin N. Fold change in evolution of proteins structures. J StructBiol 2001;134:167-85.
    • (2001) J StructBiol , vol.134 , pp. 167-185
    • Grishin, N.1
  • 3
    • 0032104477 scopus 로고    scopus 로고
    • How far divergent evolution goes in proteins
    • Murzin A. How far divergent evolution goes in proteins. Curr Opin Struct Biol 1998;8:380-7.
    • (1998) Curr Opin Struct Biol , vol.8 , pp. 380-387
    • Murzin, A.1
  • 4
    • 0042549133 scopus 로고
    • Johnson comparison of protein three-dimensional structures
    • Mark S. Johnson comparison of protein three-dimensional structures. Curr Opin Struct Biol 1991;1:334-44.
    • (1991) Curr Opin Struct Biol , vol.1 , pp. 334-344
    • Mark, S.1
  • 5
    • 9944251424 scopus 로고    scopus 로고
    • Deja vu all over again: finding and analyzing protein structure similarities
    • Sierk ML, Kleywegt GJ. Deja vu all over again: finding and analyzing protein structure similarities. Structure 2004;12: 2103-11.
    • (2004) Structure , vol.12 , pp. 2103-2111
    • Sierk, M.L.1    Kleywegt, G.J.2
  • 6
    • 1042275611 scopus 로고    scopus 로고
    • CH: structural proteomics: a tool for genome annotation
    • Yakunin AF, Yee AA, Savchenko A, et al. CH: structural proteomics: a tool for genome annotation. Curr Opin Chem Biol 2004;8:42-8.
    • (2004) Curr Opin Chem Biol , vol.8 , pp. 42-48
    • Yakunin, A.F.1    Yee, A.A.2    Savchenko, A.3
  • 7
    • 0347719528 scopus 로고    scopus 로고
    • Evaluation of protein fold comparison servers
    • Novotny M, Madsen D, Kleywegt GJ. Evaluation of protein fold comparison servers. Proteins 2004;54:260-70.
    • (2004) Proteins , vol.54 , pp. 260-270
    • Novotny, M.1    Madsen, D.2    Kleywegt, G.J.3
  • 8
    • 0024349252 scopus 로고
    • Protein structure alignment
    • Taylor W, Orengo C. Protein structure alignment. J Mol Biol 1989;208:1-22.
    • (1989) J Mol Biol , vol.208 , pp. 1-22
    • Taylor, W.1    Orengo, C.2
  • 9
    • 0030501419 scopus 로고    scopus 로고
    • Use of non-crystallographic symmetry in protein structure refinement
    • Kleywegt G. Use of non-crystallographic symmetry in protein structure refinement. Acta Crystallogr D Biol Crystallogr 1996;52:842-57.
    • (1996) Acta Crystallogr D Biol Crystallogr , vol.52 , pp. 842-857
    • Kleywegt, G.1
  • 10
    • 33746218852 scopus 로고    scopus 로고
    • MUSTANG: a multiple structural alignment algorithm
    • Konagurthu AS, Whisstock JC, Stuckey PJ, et al. MUSTANG: a multiple structural alignment algorithm. Proteins 2006;64:559-74.
    • (2006) Proteins , vol.64 , pp. 559-574
    • Konagurthu, A.S.1    Whisstock, J.C.2    Stuckey, P.J.3
  • 11
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993;233:123-38.
    • (1993) J Mol Biol , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 12
    • 0037460952 scopus 로고    scopus 로고
    • MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance
    • Jewett AI, Huang CC, Ferrin TE. MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance. Bioinformatics 2003;19:625-34.
    • (2003) Bioinformatics , vol.19 , pp. 625-634
    • Jewett, A.I.1    Huang, C.C.2    Ferrin, T.E.3
  • 13
    • 38949150854 scopus 로고    scopus 로고
    • Matt: local flexibility aids protein multiple structure alignment
    • Menke M, Berger B, Cowen L. Matt: local flexibility aids protein multiple structure alignment. PLoS Comput Biol 2008;4:e10.
    • (2008) PLoS Comput Biol , vol.4
    • Menke, M.1    Berger, B.2    Cowen, L.3
  • 14
    • 3042581007 scopus 로고    scopus 로고
    • Flexible structure alignment by chaining aligned fragment pairs allowing twists
    • Ye Y, Godzik A. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 2003; 19(Suppl. 2):ii246-55.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Ye, Y.1    Godzik, A.2
  • 15
    • 52749091256 scopus 로고    scopus 로고
    • TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model
    • Veeramalai M, Ye Y, Godzik A. "TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model". BMC Bioinformatics 2008;9: 358.
    • (2008) BMC Bioinformatics , vol.9 , pp. 358
    • Veeramalai, M.1    Ye, Y.2    Godzik, A.3
  • 16
    • 0041620359 scopus 로고    scopus 로고
    • MATRAS: a program for protein 3D structure comparison
    • Kawabata T. MATRAS: a program for protein 3D structure comparison. Nucleic Acids Res 2003;31:3367-9.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3367-3369
    • Kawabata, T.1
  • 17
    • 0025317502 scopus 로고
    • Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming
    • Sali A, Blundell TL. Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J Mol Biol 1990;212:403.
    • (1990) J Mol Biol , vol.212 , pp. 403
    • Sali, A.1    Blundell, T.L.2
  • 18
    • 38549153238 scopus 로고    scopus 로고
    • Data growth and its impact on the SCOP database: new developments
    • Andreeva A, Howorth D, Chandonia JM, et al. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 2008;36:D419-25.
    • (2008) Nucleic Acids Res , vol.36
    • Andreeva, A.1    Howorth, D.2    Chandonia, J.M.3
  • 19
    • 35448992938 scopus 로고    scopus 로고
    • Accuracy of structure-based sequence alignment of automatic methods
    • Kim C, Lee B. Accuracy of structure-based sequence alignment of automatic methods. BMCBioinformatics 2007;8:355.
    • (2007) BMCBioinformatics , vol.8 , pp. 355
    • Kim, C.1    Lee, B.2
  • 20
    • 1342289274 scopus 로고    scopus 로고
    • Sensitivity and selectivity in protein structure comparison
    • Sierk ML, Pearson WR. Sensitivity and selectivity in protein structure comparison. Protein Sci 2004;13:773-85.
    • (2004) Protein Sci , vol.13 , pp. 773-785
    • Sierk, M.L.1    Pearson, W.R.2
  • 21
    • 67949111155 scopus 로고    scopus 로고
    • Iterative refinement of structurebased sequence alignments by seed extension
    • Kim C, Tai C-H, Lee B. Iterative refinement of structurebased sequence alignments by seed extension. BMC Struct Biol 2009;10:210.
    • (2009) BMC Struct Biol , vol.10 , pp. 210
    • Kim, C.1    Tai, C.-H.2    Lee, B.3
  • 22
    • 13444279981 scopus 로고    scopus 로고
    • Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures
    • Kolodny R, Koehl P, Levitt M. Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. JMol Biol 2005;346:1173-88.
    • (2005) JMol Biol , vol.346 , pp. 1173-1188
    • Kolodny, R.1    Koehl, P.2    Levitt, M.3
  • 23
    • 4544295055 scopus 로고    scopus 로고
    • Detecting local structural similarity in proteins by maximizing number of equivalent residues
    • Standley DM, Toh H, Nakamura H. Detecting local structural similarity in proteins by maximizing number of equivalent residues. Proteins 2004;57:381-91.
    • (2004) Proteins , vol.57 , pp. 381-391
    • Standley, D.M.1    Toh, H.2    Nakamura, H.3
  • 24
    • 0029982530 scopus 로고    scopus 로고
    • The structural alignment between two proteins: is there a unique answer?
    • Godzik A. The structural alignment between two proteins: is there a unique answer? Protein Sci 1996;5:1325-38.
    • (1996) Protein Sci , vol.5 , pp. 1325-1338
    • Godzik, A.1
  • 25
    • 34548304928 scopus 로고    scopus 로고
    • Comparative analysis of protein structure alignments
    • Mayr G, Domingues FS, Lackner P. Comparative analysis of protein structure alignments. BMC Struct Biol 2007;7:50.
    • (2007) BMC Struct Biol , vol.7 , pp. 50
    • Mayr, G.1    Domingues, F.S.2    Lackner, P.3
  • 26
    • 0036304230 scopus 로고    scopus 로고
    • Protein fold similarity estimated by a probabilistic approach based on Cα-Cα distance comparison
    • Carugo O, Pongor S. Protein fold similarity estimated by a probabilistic approach based on Cα-Cα distance comparison. J Mol Biol 2002;315:887-98.
    • (2002) J Mol Biol , vol.315 , pp. 887-898
    • Carugo, O.1    Pongor, S.2
  • 27
    • 0037422619 scopus 로고    scopus 로고
    • Automatic classification of protein structure by using Gauss integrals
    • Rogen P, Fain B. Automatic classification of protein structure by using Gauss integrals. Proc Natl Acad Sci USA 2003; 100:119-24.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 119-124
    • Rogen, P.1    Fain, B.2
  • 28
    • 0028087774 scopus 로고
    • MALIGN: a multiple sequence alignment program
    • Wheeler WC. MALIGN: a multiple sequence alignment program. J Heredity 1994;85:419-20.
    • (1994) J Heredity , vol.85 , pp. 419-420
    • Wheeler, W.C.1
  • 29
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988;85: 2444-8.
    • (1988) Proc Natl Acad Sci USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 30
    • 0043123123 scopus 로고    scopus 로고
    • Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments
    • Poirot O, O'Toole E, Notredame C. Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res 2003;31: 3503-6.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3503-3506
    • Poirot, O.1    O'Toole, E.2    Notredame, C.3
  • 32
    • 0031714858 scopus 로고    scopus 로고
    • JOY: protein sequence-structure representation and analysis
    • Mizuguchi K, Deane CM, Blundell TL, et al. JOY: protein sequence-structure representation and analysis. Bioinformatics 1998;14:617-23.
    • (1998) Bioinformatics , vol.14 , pp. 617-623
    • Mizuguchi, K.1    Deane, C.M.2    Blundell, T.L.3
  • 33
    • 17144386527 scopus 로고
    • Box-and-Whisker Plots. §2C in Exploratory Data Analysis
    • MA: Addison-Wesley
    • Tukey JW. Box-and-Whisker Plots. §2C in Exploratory Data Analysis. Reading, MA: Addison-Wesley, 1977,39-43.
    • (1977) Reading , pp. 39-43
    • Tukey, J.W.1
  • 34
    • 0017844356 scopus 로고
    • Amino acid sequence alignment of bacterial and mammalian pancreatic serine proteases based on topological equivalences
    • James MNG, Delbaere LTJ, Brayer GD. Amino acid sequence alignment of bacterial and mammalian pancreatic serine proteases based on topological equivalences. Can J Biochem 1978;56:396-402.
    • (1978) Can J Biochem , vol.56 , pp. 396-402
    • James, M.N.G.1    Delbaere, L.T.J.2    Brayer, G.D.3
  • 35
    • 0021766631 scopus 로고
    • Critical evaluation of comparative model building of streptomyces griseus trypsin
    • Read RJ, Brayer GD, Jurasek L, et al. Critical evaluation of comparative model building of streptomyces griseus trypsin. Biochemistry 1984;23:6570-5.
    • (1984) Biochemistry , vol.23 , pp. 6570-6575
    • Read, R.J.1    Brayer, G.D.2    Jurasek, L.3
  • 36
    • 0036882394 scopus 로고    scopus 로고
    • Serine protease mechanism and specificity
    • Hedstrom L. Serine protease mechanism and specificity. Chem Rev 2002;102:4501-24.
    • (2002) Chem Rev , vol.102 , pp. 4501-4524
    • Hedstrom, L.1
  • 37
    • 0038146970 scopus 로고    scopus 로고
    • Peptide ligands for the fibronectin type II modules of matrix metalloproteinase 2 (MMP-2)
    • Trexler M, Briknarová K, Gehrmann M, et al. Peptide ligands for the fibronectin type II modules of matrix metalloproteinase 2 (MMP-2). J Biol Chem 2003;278: 12241-6.
    • (2003) J Biol Chem , vol.278 , pp. 12241-12246
    • Trexler, M.1    Briknarová, K.2    Gehrmann, M.3
  • 38
    • 0032988850 scopus 로고    scopus 로고
    • BaliBASE: a benchmark alignment database for the evaluation of multiple sequence alignment programs
    • Thompson JD, Plewniak F, Poch O. BaliBASE: a benchmark alignment database for the evaluation of multiple sequence alignment programs. Bioinformatics 1999; 1:87-8.
    • (1999) Bioinformatics , vol.1 , pp. 87-88
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.