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Volumn 8, Issue , 2007, Pages

Protein structural similarity search by Ramachandran codes

Author keywords

[No Author keywords available]

Indexed keywords

DATABASE SEARCHES; EXPECTATION VALUES; FUNCTIONAL ANNOTATION; HOMOLOGOUS STRUCTURES; PROTEIN STRUCTURES; SEQUENCE ALIGNMENT METHODS; SEQUENCE SIMILARITY; STRUCTURAL SIMILARITY;

EID: 38049165999     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-307     Document Type: Article
Times cited : (46)

References (54)
  • 1
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • 1166865 3709526
    • Chothia C Lesk AM The relation between the divergence of sequence and structure in proteins Embo J 1986, 5(4):823-826. 1166865 3709526
    • (1986) Embo J , vol.5 , Issue.4 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 2
    • 0032104477 scopus 로고    scopus 로고
    • How far divergent evolution goes in proteins
    • 10.1016/S0959-440X(98)80073-0 9666335
    • Murzin AG How far divergent evolution goes in proteins Curr Opin Struct Biol 1998, 8(3):380-387. 10.1016/S0959-440X(98)80073-0 9666335
    • (1998) Curr Opin Struct Biol , vol.8 , Issue.3 , pp. 380-387
    • Murzin, A.G.1
  • 3
    • 0034237578 scopus 로고    scopus 로고
    • Large-scale comparison of protein sequence alignment algorithms with structure alignments
    • 10.1002/(SICI)1097-0134(20000701)40:1<6::AID-PROT30>3.0.CO;2-7 10813826
    • Sauder JM Arthur JW Dunbrack RL Jr. Large-scale comparison of protein sequence alignment algorithms with structure alignments Proteins 2000, 40(1):6-22. 10.1002/(SICI)1097-0134(20000701)40:1<6::AID- PROT30>3.0.CO;2-7 10813826
    • (2000) Proteins , vol.40 , Issue.1 , pp. 6-22
    • Sauder, J.M.1    Arthur, J.W.2    Dunbrack Jr., R.L.3
  • 4
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • 10.1006/jmbi.1993.1489 8377180
    • Holm L Sander C Protein structure comparison by alignment of distance matrices J Mol Biol 1993, 233(1):123-138. 10.1006/jmbi.1993.1489 8377180
    • (1993) J Mol Biol , vol.233 , Issue.1 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 5
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • 10.1093/protein/11.9.739 9796821
    • Shindyalov IN Bourne PE Protein structure alignment by incremental combinatorial extension (CE) of the optimal path Protein Eng 1998, 11(9):739-747. 10.1093/protein/11.9.739 9796821
    • (1998) Protein Eng , vol.11 , Issue.9 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 6
    • 12944271968 scopus 로고    scopus 로고
    • FAST: A novel protein structure alignment algorithm
    • 10.1002/prot.20331 15609341
    • Zhu J Weng Z FAST: A novel protein structure alignment algorithm Proteins 2005, 58(3):618-627. 10.1002/prot.20331 15609341
    • (2005) Proteins , vol.58 , Issue.3 , pp. 618-627
    • Zhu, J.1    Weng, Z.2
  • 7
    • 0025876842 scopus 로고
    • Energetic approach to the folding of alpha/beta barrels
    • 10.1002/prot.340090406 1866432
    • Chou KC Carlacci L Energetic approach to the folding of alpha/beta barrels Proteins 1991, 9(4):280-295. 10.1002/prot.340090406 1866432
    • (1991) Proteins , vol.9 , Issue.4 , pp. 280-295
    • Chou, K.C.1    Carlacci, L.2
  • 8
    • 0342517321 scopus 로고
    • Structural principles of parallel beta-barrels in proteins
    • 280204 3368445 10.1073/pnas.85.10.3338
    • Lasters I Wodak SJ Alard P van Cutsem E Structural principles of parallel beta-barrels in proteins Proc Natl Acad Sci U S A 1988, 85(10):3338-3342. 280204 3368445 10.1073/pnas.85.10.3338
    • (1988) Proc Natl Acad Sci U S A , vol.85 , Issue.10 , pp. 3338-3342
    • Lasters, I.1    Wodak, S.J.2    Alard, P.3    van Cutsem, E.4
  • 9
    • 0025372503 scopus 로고
    • The design of idealized alpha/beta-barrels: Analysis of beta-sheet closure requirements
    • 10.1002/prot.340070306 2362946
    • Lasters I Wodak SJ Pio F The design of idealized alpha/beta-barrels: analysis of beta-sheet closure requirements Proteins 1990, 7(3):249-256. 10.1002/prot.340070306 2362946
    • (1990) Proteins , vol.7 , Issue.3 , pp. 249-256
    • Lasters, I.1    Wodak, S.J.2    Pio, F.3
  • 10
    • 0028348081 scopus 로고
    • Principles determining the structure of beta-sheet barrels in proteins. I. A theoretical analysis
    • 10.1016/0022-2836(94)90064-7 8126726
    • Murzin AG Lesk AM Chothia C Principles determining the structure of beta-sheet barrels in proteins. I. A theoretical analysis J Mol Biol 1994, 236(5):1369-1381. 10.1016/0022-2836(94)90064-7 8126726
    • (1994) J Mol Biol , vol.236 , Issue.5 , pp. 1369-1381
    • Murzin, A.G.1    Lesk, A.M.2    Chothia, C.3
  • 12
    • 0022357447 scopus 로고
    • Amino acid composition and hydrophobicity patterns of protein domains correlate with their structures
    • 10.1002/bip.360241011 4074850
    • Sheridan RP Dixon JS Venkataraghavan R Kuntz ID Scott KP Amino acid composition and hydrophobicity patterns of protein domains correlate with their structures Biopolymers 1985, 24(10):1995-2023. 10.1002/ bip.360241011 4074850
    • (1985) Biopolymers , vol.24 , Issue.10 , pp. 1995-2023
    • Sheridan, R.P.1    Dixon, J.S.2    Venkataraghavan, R.3    Kuntz, I.D.4    Scott, K.P.5
  • 13
    • 0025275776 scopus 로고
    • Use of techniques derived from graph theory to compare secondary structure motifs in proteins
    • 10.1016/0022-2836(90)90312-A 2319595
    • Mitchell EM Artymiuk PJ Rice DW Willett P Use of techniques derived from graph theory to compare secondary structure motifs in proteins J Mol Biol 1990, 212(1):151-166. 10.1016/0022-2836(90)90312-A 2319595
    • (1990) J Mol Biol , vol.212 , Issue.1 , pp. 151-166
    • Mitchell, E.M.1    Artymiuk, P.J.2    Rice, D.W.3    Willett, P.4
  • 14
    • 84944813497 scopus 로고
    • A method for the systematic comparison of the three-dimensional structures of proteins and some results
    • Levine M Stuart D Williams J A method for the systematic comparison of the three-dimensional structures of proteins and some results Acta Cryst 1984, A40:600-610.
    • (1984) Acta Cryst , vol.A40 , pp. 600-610
    • Levine, M.1    Stuart, D.2    Williams, J.3
  • 15
    • 0027428284 scopus 로고
    • Standard structures in proteins
    • 10.1016/0079-6107(93)90015-C 8372226
    • Efimov AV Standard structures in proteins Prog Biophys Mol Biol 1993, 60(3):201-239. 10.1016/0079-6107(93)90015-C 8372226
    • (1993) Prog Biophys Mol Biol , vol.60 , Issue.3 , pp. 201-239
    • Efimov, A.V.1
  • 16
    • 38049125203 scopus 로고    scopus 로고
    • Application of sequence alignment methods to multiple structural alignment and superposition
    • Lesk AM Application of sequence alignment methods to multiple structural alignment and superposition Proceedings of Prague Stringology Club Workshop '98 Prague 1998, 95-100.
    • (1998) Proceedings of Prague Stringology Club Workshop '98 , pp. 95-100
    • Lesk, A.M.1
  • 17
    • 0034458972 scopus 로고    scopus 로고
    • The ups and downs of protein topology; rapid comparison of protein structure
    • 10.1093/protein/13.12.829 11239082
    • Martin AC The ups and downs of protein topology; rapid comparison of protein structure Protein Eng 2000, 13(12):829-837. 10.1093/protein/ 13.12.829 11239082
    • (2000) Protein Eng , vol.13 , Issue.12 , pp. 829-837
    • Martin, A.C.1
  • 18
    • 3242891058 scopus 로고    scopus 로고
    • SA-Search: A web tool for protein structure mining based on a Structural Alphabet
    • 441605 15215446 10.1093/nar/gkh467
    • Guyon F Camproux AC Hochez J Tuffery P SA-Search: A web tool for protein structure mining based on a Structural Alphabet Nucleic Acids Res 2004 32 Web Server issue W545-8. 441605 15215446 10.1093/nar/gkh467
    • (2004) Nucleic Acids Res , vol.32
    • Guyon, F.1    Camproux, A.C.2    Hochez, J.3    Tuffery, P.4
  • 19
    • 0035967880 scopus 로고    scopus 로고
    • FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
    • 10.1006/jmbi.2001.4762 11419950
    • Shi J Blundell TL Mizuguchi K FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties J Mol Biol 2001, 310(1):243-257. 10.1006/jmbi.2001.4762 11419950
    • (2001) J Mol Biol , vol.310 , Issue.1 , pp. 243-257
    • Shi, J.1    Blundell, T.L.2    Mizuguchi, K.3
  • 20
    • 0034595501 scopus 로고    scopus 로고
    • Enhanced genome annotation using structural profiles in the program 3D-PSSM
    • 10.1006/jmbi.2000.3741 10860755
    • Kelley LA MacCallum RM Sternberg MJ Enhanced genome annotation using structural profiles in the program 3D-PSSM J Mol Biol 2000, 299(2):499-520. 10.1006/jmbi.2000.3741 10860755
    • (2000) J Mol Biol , vol.299 , Issue.2 , pp. 499-520
    • Kelley, L.A.1    MacCallum, R.M.2    Sternberg, M.J.3
  • 21
    • 24344476038 scopus 로고    scopus 로고
    • YAKUSA: A fast structural database scanning method
    • 10.1002/prot.20517 16049912
    • Carpentier M Brouillet S Pothier J YAKUSA: A fast structural database scanning method Proteins 2005, 61(1):137-151. 10.1002/prot.20517 16049912
    • (2005) Proteins , vol.61 , Issue.1 , pp. 137-151
    • Carpentier, M.1    Brouillet, S.2    Pothier, J.3
  • 22
    • 33747096251 scopus 로고    scopus 로고
    • Protein structure database search and evolutionary classification
    • 1540718 16885238 10.1093/nar/gkl395
    • Yang JM Tung CH Protein structure database search and evolutionary classification Nucleic Acids Res 2006, 34(13):3646-3659. 1540718 16885238 10.1093/nar/gkl395
    • (2006) Nucleic Acids Res , vol.34 , Issue.13 , pp. 3646-3659
    • Yang, J.M.1    Tung, C.H.2
  • 23
    • 33748280492 scopus 로고    scopus 로고
    • A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications
    • 10.1002/prot.21087 16894618
    • Tyagi M Gowri VS Srinivasan N de Brevern AG Offmann B A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications Proteins 2006, 65(1):32-39. 10.1002/prot.21087 16894618
    • (2006) Proteins , vol.65 , Issue.1 , pp. 32-39
    • Tyagi, M.1    Gowri, V.S.2    Srinivasan, N.3    de Brevern, A.G.4    Offmann, B.5
  • 25
    • 0034669774 scopus 로고    scopus 로고
    • Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks
    • 10.1002/1097-0134(20001115)41:3<271::AID-PROT10>3.0.CO;2-Z 11025540
    • de Brevern AG Etchebest C Hazout S Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks Proteins 2000, 41(3):271-287. 10.1002/1097-0134(20001115)41:3<271::AID- PROT10>3.0.CO;2-Z 11025540
    • (2000) Proteins , vol.41 , Issue.3 , pp. 271-287
    • de Brevern, A.G.1    Etchebest, C.2    Hazout, S.3
  • 26
    • 18844454820 scopus 로고    scopus 로고
    • A structural alphabet for local protein structures: Improved prediction methods
    • 10.1002/prot.20458 15822101
    • Etchebest C Benros C Hazout S de Brevern AG A structural alphabet for local protein structures: Improved prediction methods Proteins 2005, 59(4):810-827. 10.1002/prot.20458 15822101
    • (2005) Proteins , vol.59 , Issue.4 , pp. 810-827
    • Etchebest, C.1    Benros, C.2    Hazout, S.3    de Brevern, A.G.4
  • 27
    • 33947526348 scopus 로고    scopus 로고
    • "Pinning strategy": A novel approach for predicting the backbone structure in terms of protein blocks from sequence
    • 10.1007/s12038-007-0006-3 17426380
    • De Brevern AG Etchebest C Benros C Hazout S "Pinning strategy": A novel approach for predicting the backbone structure in terms of protein blocks from sequence J Biosci 2007, 32(1):51-70. 10.1007/s12038-007-0006-3 17426380
    • (2007) J Biosci , vol.32 , Issue.1 , pp. 51-70
    • De Brevern, A.G.1    Etchebest, C.2    Benros, C.3    Hazout, S.4
  • 29
    • 0014381393 scopus 로고
    • Conformation of polypeptides and proteins
    • 4882249
    • Ramachandran GN Sasisekharan V Conformation of polypeptides and proteins Adv Protein Chem 1968, 23:283-438. 4882249
    • (1968) Adv Protein Chem , vol.23 , pp. 283-438
    • Ramachandran, G.N.1    Sasisekharan, V.2
  • 30
    • 2442645157 scopus 로고    scopus 로고
    • Rapid 3D protein structure database searching using information retrieval techniques
    • 10.1093/bioinformatics/bth036 14962928
    • Aung Z Tan KL Rapid 3D protein structure database searching using information retrieval techniques Bioinformatics 2004, 20(7):1045-1052. 10.1093/bioinformatics/bth036 14962928
    • (2004) Bioinformatics , vol.20 , Issue.7 , pp. 1045-1052
    • Aung, Z.1    Tan, K.L.2
  • 32
    • 0033977581 scopus 로고    scopus 로고
    • The ASTRAL compendium for protein structure and sequence analysis
    • 102434 10592239 10.1093/nar/28.1.254
    • Brenner SE Koehl P Levitt M The ASTRAL compendium for protein structure and sequence analysis Nucleic Acids Res 2000, 28(1):254-256. 102434 10592239 10.1093/nar/28.1.254
    • (2000) Nucleic Acids Res , vol.28 , Issue.1 , pp. 254-256
    • Brenner, S.E.1    Koehl, P.2    Levitt, M.3
  • 37
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • 146917 9254694 10.1093/nar/25.17.3389
    • Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997, 25(17):3389-3402. 146917 9254694 10.1093/nar/25.17.3389
    • (1997) Nucleic Acids Res , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 38
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • 50453 1438297 10.1073/pnas.89.22.10915
    • Henikoff S Henikoff JG Amino acid substitution matrices from protein blocks Proc Natl Acad Sci U S A 1992, 89(22):10915-10919. 50453 1438297 10.1073/pnas.89.22.10915
    • (1992) Proc Natl Acad Sci U S A , vol.89 , Issue.22 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 39
    • 18044385763 scopus 로고    scopus 로고
    • Agreement, the f-measure, and reliability in information retrieval
    • 1090460 15684123 10.1197/jamia.M1733
    • Hripcsak G Rothschild AS Agreement, the f-measure, and reliability in information retrieval J Am Med Inform Assoc 2005, 12(3):296-298. 1090460 15684123 10.1197/jamia.M1733
    • (2005) J Am Med Inform Assoc , vol.12 , Issue.3 , pp. 296-298
    • Hripcsak, G.1    Rothschild, A.S.2
  • 44
    • 2442592993 scopus 로고    scopus 로고
    • A hidden markov model derived structural alphabet for proteins
    • 10.1016/j.jmb.2004.04.005 15147844
    • Camproux AC Gautier R Tuffery P A hidden markov model derived structural alphabet for proteins J Mol Biol 2004, 339(3):591-605. 10.1016/ j.jmb.2004.04.005 15147844
    • (2004) J Mol Biol , vol.339 , Issue.3 , pp. 591-605
    • Camproux, A.C.1    Gautier, R.2    Tuffery, P.3
  • 45
    • 0033405214 scopus 로고    scopus 로고
    • Hidden Markov model approach for identifying the modular framework of the protein backbone
    • 10.1093/protein/12.12.1063 10611400
    • Camproux AC Tuffery P Chevrolat JP Boisvieux JF Hazout S Hidden Markov model approach for identifying the modular framework of the protein backbone Protein Eng 1999, 12(12):1063-1073. 10.1093/protein/12.12.1063 10611400
    • (1999) Protein Eng , vol.12 , Issue.12 , pp. 1063-1073
    • Camproux, A.C.1    Tuffery, P.2    Chevrolat, J.P.3    Boisvieux, J.F.4    Hazout, S.5
  • 46
    • 0029889221 scopus 로고    scopus 로고
    • Local alignment statistics
    • 8743700
    • Altschul SF Gish W Local alignment statistics Methods Enzymol 1996, 266:460-480. 8743700
    • (1996) Methods Enzymol , vol.266 , pp. 460-480
    • Altschul, S.F.1    Gish, W.2
  • 47
    • 0032509105 scopus 로고    scopus 로고
    • Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
    • 10.1006/jmbi.1998.2221 9837738
    • Park J Karplus K Barrett C Hughey R Haussler D Hubbard T Chothia C Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods J Mol Biol 1998, 284(4):1201-1210. 10.1006/jmbi.1998.2221 9837738
    • (1998) J Mol Biol , vol.284 , Issue.4 , pp. 1201-1210
    • Park, J.1    Karplus, K.2    Barrett, C.3    Hughey, R.4    Haussler, D.5    Hubbard, T.6    Chothia, C.7
  • 48
    • 0036499870 scopus 로고    scopus 로고
    • Automated assignment of SCOP and CATH protein structure classifications from FSSP scores
    • 10.1002/prot.1176 11835515
    • Getz G Vendruscolo M Sachs D Domany E Automated assignment of SCOP and CATH protein structure classifications from FSSP scores Proteins 2002, 46(4):405-415. 10.1002/prot.1176 11835515
    • (2002) Proteins , vol.46 , Issue.4 , pp. 405-415
    • Getz, G.1    Vendruscolo, M.2    Sachs, D.3    Domany, E.4
  • 49
    • 0027991446 scopus 로고
    • The FSSP database of structurally aligned protein fold families
    • 308329 7937067
    • Holm L Sander C The FSSP database of structurally aligned protein fold families Nucleic Acids Res 1994, 22(17):3600-3609. 308329 7937067
    • (1994) Nucleic Acids Res , vol.22 , Issue.17 , pp. 3600-3609
    • Holm, L.1    Sander, C.2
  • 50
    • 0029976603 scopus 로고    scopus 로고
    • Using CLUSTAL for multiple sequence alignments
    • 8743695
    • Higgins DG Thompson JD Gibson TJ Using CLUSTAL for multiple sequence alignments Methods Enzymol 1996, 266:383-402. 8743695
    • (1996) Methods Enzymol , vol.266 , pp. 383-402
    • Higgins, D.G.1    Thompson, J.D.2    Gibson, T.J.3
  • 51
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • 308517 7984417 10.1093/nar/22.22.4673
    • Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 1994, 22(22):4673-4680. 308517 7984417 10.1093/nar/22.22.4673
    • (1994) Nucleic Acids Res , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 54
    • 0030339738 scopus 로고    scopus 로고
    • AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
    • 10.1007/BF00228148 9008363
    • Laskowski RA Rullmannn JA MacArthur MW Kaptein R Thornton JM AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR J Biomol NMR 1996, 8(4):477-486. 10.1007/BF00228148 9008363
    • (1996) J Biomol NMR , vol.8 , Issue.4 , pp. 477-486
    • Laskowski, R.A.1    Rullmannn, J.A.2    MacArthur, M.W.3    Kaptein, R.4    Thornton, J.M.5


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