메뉴 건너뛰기




Volumn 6, Issue 1, 2008, Pages 163-181

TAli: Local alignment of protein structures using backbone torsion angles

Author keywords

Backbone torsion angles; Homolog identification; Protein evolution; Protein structure; Structural alignment

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE;

EID: 37049039413     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720008003370     Document Type: Conference Paper
Times cited : (22)

References (34)
  • 2
    • 44049083028 scopus 로고    scopus 로고
    • Zhu B, On the complexity of protein local structure alignment under the discrete Frechet distance, arXiv:0709.0677, 2007.
    • Zhu B, On the complexity of protein local structure alignment under the discrete Frechet distance, arXiv:0709.0677, 2007.
  • 4
    • 0033990061 scopus 로고    scopus 로고
    • Flexible sequence similarity searching with the FASTA3 program package
    • Pearson WR, Flexible sequence similarity searching with the FASTA3 program package, Methods Mol Biol 132:185-219, 2000.
    • (2000) Methods Mol Biol , vol.132 , pp. 185-219
    • Pearson, W.R.1
  • 5
    • 17644392830 scopus 로고    scopus 로고
    • A protein structure alignment algorithm based on the TM-score
    • Zhang Y, Skolnick J, TM-align: A protein structure alignment algorithm based on the TM-score, Nucleic Acids Res 33(7):2302-2309, 2005.
    • (2005) Nucleic Acids Res , vol.33 , Issue.7 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2    align, T.3
  • 6
    • 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 233(1):123-138, 1993.
    • (1993) J Mol Biol , vol.233 , Issue.1 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 7
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov IN, Bourne PE, Protein structure alignment by incremental combinatorial extension (CE) of the optimal path, Protein Eng 11(9):739-747, 1998.
    • (1998) Protein Eng , vol.11 , Issue.9 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 8
    • 13444307044 scopus 로고    scopus 로고
    • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    • Pt 1
    • Krissinel E, Henrick K, Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions, Acta Crystallogr D Biol Crystallogr 60(Pt 12 Pt 1):2256-2268, 2004.
    • (2004) Acta Crystallogr D Biol Crystallogr , vol.60 , Issue.PART 12 , pp. 2256-2268
    • Krissinel, E.1    Henrick, K.2
  • 10
    • 3242888280 scopus 로고    scopus 로고
    • ProteinDBS: A real-time retrieval system for protein structure comparison
    • Web Server issue:W572-W575
    • Shyu C-R, Chi P-H, Scott G, Xu D, ProteinDBS: A real-time retrieval system for protein structure comparison, Nucleic Acids Res 32 Web Server issue):W572-W575, 2004.
    • (2004) Nucleic Acids Res , vol.32
    • Shyu, C.-R.1    Chi, P.-H.2    Scott, G.3    Xu, D.4
  • 11
    • 1842450688 scopus 로고    scopus 로고
    • FlexProt: Alignment of flexible protein structures without a predefinition of hinge regions
    • Shatsky M, Nussinov R, Wolfson HJ, FlexProt: Alignment of flexible protein structures without a predefinition of hinge regions, J Comput Biol 11(1):83-106, 2004.
    • (2004) J Comput Biol , vol.11 , Issue.1 , pp. 83-106
    • Shatsky, M.1    Nussinov, R.2    Wolfson, H.J.3
  • 12
    • 3242887315 scopus 로고    scopus 로고
    • FATCAT: A web server for flexible structure comparison and structure similarity searching
    • Web Server issue:W582-W585
    • Ye Y, Godzik A, FATCAT: A web server for flexible structure comparison and structure similarity searching, Nucleic Acids Res 32(Web Server issue):W582-W585, 2004.
    • (2004) Nucleic Acids Res , vol.32
    • Ye, Y.1    Godzik, A.2
  • 13
    • 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 100(1):119-124, 2003.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.1 , pp. 119-124
    • Rogen, P.1    Fain, B.2
  • 14
    • 0242585484 scopus 로고    scopus 로고
    • A new family of global protein shape descriptors
    • Rogen P, Bohr H, A new family of global protein shape descriptors, Math Biosci 182(2):167-181, 2003.
    • (2003) Math Biosci , vol.182 , Issue.2 , pp. 167-181
    • Rogen, P.1    Bohr, H.2
  • 15
    • 27544483936 scopus 로고    scopus 로고
    • CHORAL: A differential geometry approach to the prediction of the cores of protein structures
    • Montalvao RW, Smith RE, Lovell SC, Blundell TL, CHORAL: A differential geometry approach to the prediction of the cores of protein structures, Bioinformatics 21(19):3719-3725, 2005.
    • (2005) Bioinformatics , vol.21 , Issue.19 , pp. 3719-3725
    • Montalvao, R.W.1    Smith, R.E.2    Lovell, S.C.3    Blundell, T.L.4
  • 16
    • 33748374227 scopus 로고    scopus 로고
    • Structure alignment based on coding of local geometric measures
    • Chang PL, Rinne AW, Dewey TG, Structure alignment based on coding of local geometric measures, BMC Bioinformatics 7:346, 2006.
    • (2006) BMC Bioinformatics , vol.7 , pp. 346
    • Chang, P.L.1    Rinne, A.W.2    Dewey, T.G.3
  • 17
    • 0019887799 scopus 로고
    • Identification of common moleculax subsequences
    • Smith TF, Waterman MS, Identification of common moleculax subsequences, J Mol Biol 147(1):195-197, 1981.
    • (1981) J Mol Biol , vol.147 , Issue.1 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 18
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman SB, Wunsch CD, A general method applicable to the search for similarities in the amino acid sequence of two proteins, J Mol Biol 48(3):443-453, 1970.
    • (1970) J Mol Biol , vol.48 , Issue.3 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 19
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski R, MacArthur M, Moss D, Thornton J, PROCHECK: A program to check the stereochemical quality of protein structures, J Appl Cryst 26:283-291, 1993.
    • (1993) J Appl Cryst , vol.26 , pp. 283-291
    • Laskowski, R.1    MacArthur, M.2    Moss, D.3    Thornton, J.4
  • 21
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, Nei M, The neighbor-joining method: A new method for reconstructing phylogenetic trees, Mol Biol Evol 4 4):406-425, 1987.
    • (1987) Mol Biol Evol , vol.4 , Issue.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 22
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • Hillis DM, Mortz C, Mable B eds, 2nd ed, Sinauer Associates, Sunderland, MA, pp
    • Swofford DL, Olsen GJ, Waddell PJ, Hillis DM, Phylogenetic inference, in Hillis DM, Mortz C, Mable B (eds.), Molecular Systematics, 2nd ed., Sinauer Associates, Sunderland, MA, pp. 407-514, 1996.
    • (1996) Molecular Systematics , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 24
    • 0030310317 scopus 로고    scopus 로고
    • Assessing the performance of fold recognition methods by rpeans of a comprehensive benchmark
    • Fischer D, Elofsson A, Rice D, Eisenberg D, Assessing the performance of fold recognition methods by rpeans of a comprehensive benchmark, Pac Symp Biocomput, pp. 300-318, 1996.
    • (1996) Pac Symp Biocomput , pp. 300-318
    • Fischer, D.1    Elofsson, A.2    Rice, D.3    Eisenberg, D.4
  • 25
    • 0024066065 scopus 로고
    • The 2.0 Å X-ray crystal structure of chicken egg white cystatin and its possible mode of interaction with cysteine proteinases
    • Bode W, Engh R, Musil D, Thiele U, Huber R, Karshikov A, Brzin J, Kos J, Turk V, The 2.0 Å X-ray crystal structure of chicken egg white cystatin and its possible mode of interaction with cysteine proteinases, EMBO J 7(8):2593-2599, 1988.
    • (1988) EMBO J , vol.7 , Issue.8 , pp. 2593-2599
    • Bode, W.1    Engh, R.2    Musil, D.3    Thiele, U.4    Huber, R.5    Karshikov, A.6    Brzin, J.7    Kos, J.8    Turk, V.9
  • 26
    • 0027527431 scopus 로고
    • Two crystal structures of a potently sweet protein. Natural monellin at 2.75 Å resolution and single-chain monellin at 1.7 Å resolution
    • Somoza JR, Jiang F, Tong L, Kang CH, Cho JM, Kim SH, Two crystal structures of a potently sweet protein. Natural monellin at 2.75 Å resolution and single-chain monellin at 1.7 Å resolution, J Mol Biol 234(2):390-404, 1993.
    • (1993) J Mol Biol , vol.234 , Issue.2 , pp. 390-404
    • Somoza, J.R.1    Jiang, F.2    Tong, L.3    Kang, C.H.4    Cho, J.M.5    Kim, S.H.6
  • 27
  • 29
    • 0033548581 scopus 로고    scopus 로고
    • Glycyl-tRNA synthetase uses a negatively charged pit for specific recognition and activation of glycine
    • Arnez JG, Dock-Bregeon AC, Moras D, Glycyl-tRNA synthetase uses a negatively charged pit for specific recognition and activation of glycine, J Mol Biol 286(5):1449-1459, 1999.
    • (1999) J Mol Biol , vol.286 , Issue.5 , pp. 1449-1459
    • Arnez, J.G.1    Dock-Bregeon, A.C.2    Moras, D.3
  • 30
    • 0346848759 scopus 로고    scopus 로고
    • On the evolution of structure in aminoacyl-tRNA synthetases
    • O'Donoghue P, Luthey-Schulten Z, On the evolution of structure in aminoacyl-tRNA synthetases, Microbiol Mol Biol Rev 67 4):550-573, 2003.
    • (2003) Microbiol Mol Biol Rev , vol.67 , Issue.4 , pp. 550-573
    • O'Donoghue, P.1    Luthey-Schulten, Z.2
  • 31
    • 16244404569 scopus 로고    scopus 로고
    • Molecular fragment replacement approach to protein structure determination by chemical shift and dipolax homology database mining
    • Kontaxis G, Delaglio F, Bax A, Molecular fragment replacement approach to protein structure determination by chemical shift and dipolax homology database mining, Methods Enzymol 394:42-78, 2005.
    • (2005) Methods Enzymol , vol.394 , pp. 42-78
    • Kontaxis, G.1    Delaglio, F.2    Bax, A.3
  • 32
    • 3242887695 scopus 로고    scopus 로고
    • Protein structure prediction and analysis using the Robetta server
    • Web Server issue:W526-W531
    • Kim DE, Chivian D, Baker D, Protein structure prediction and analysis using the Robetta server, Nucleic Acids Res 32(Web Server issue):W526-W531, 2004.
    • (2004) Nucleic Acids Res , vol.32
    • Kim, D.E.1    Chivian, D.2    Baker, D.3
  • 33
    • 0032104477 scopus 로고    scopus 로고
    • How far divergent evolution goes in proteins
    • Murzin AG, How far divergent evolution goes in proteins, Curr Opin Struct Biol 8(3):380-387, 1998.
    • (1998) Curr Opin Struct Biol , vol.8 , Issue.3 , pp. 380-387
    • Murzin, A.G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.