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Volumn 61, Issue SUPPL. 7, 2005, Pages 157-166

Prediction of CASP6 structures using automated Robetta protocols

Author keywords

De novo modeling; Fragment assembly; Homology modeling; Parametric alignment ensemble; Rosetta

Indexed keywords

PROTEIN;

EID: 30344443955     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20733     Document Type: Conference Paper
Times cited : (124)

References (46)
  • 2
    • 0242299187 scopus 로고    scopus 로고
    • Predictions without templates: New folds, secondary structure, and contacts in CASP5
    • Aloy P, Stark A, Hadley C, Russell RB. Predictions without templates: new folds, secondary structure, and contacts in CASP5. Proteins 2003;Suppl 6:436-456.
    • (2003) Proteins , Issue.SUPPL. 6 , pp. 436-456
    • Aloy, P.1    Stark, A.2    Hadley, C.3    Russell, R.B.4
  • 3
    • 0242299155 scopus 로고    scopus 로고
    • CAFASP3: The third critical assessment of fully automated structure prediction methods
    • Fischer D, Rychlewski L, Dunbrack Jr. RL, Ortiz AR, Elofsson A. CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins 2003;Suppl 6:503-516.
    • (2003) Proteins , Issue.SUPPL. 6 , pp. 503-516
    • Fischer, D.1    Rychlewski, L.2    Dunbrack Jr., R.L.3    Ortiz, A.R.4    Elofsson, A.5
  • 5
    • 3242887695 scopus 로고    scopus 로고
    • Protein structure prediction and analysis using the Robetta server
    • Kim DE, Chivian D, Baker D. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res 2004;32(Web Server issue):W526-531.
    • (2004) Nucleic Acids Res , vol.32 , Issue.WEB SERVER ISSUE
    • Kim, D.E.1    Chivian, D.2    Baker, D.3
  • 6
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997;268:209-225.
    • (1997) J Mol Biol , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 7
    • 0032929780 scopus 로고    scopus 로고
    • Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
    • Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 1999;34:82-95.
    • (1999) Proteins , vol.34 , pp. 82-95
    • Simons, K.T.1    Ruczinski, I.2    Kooperberg, C.3    Fox, B.A.4    Bystroff, C.5    Baker, D.6
  • 8
    • 0014694384 scopus 로고
    • Tertiary structure of Escherichia coli beta-D-galactosidase
    • Goldberg ME. Tertiary structure of Escherichia coli beta-D-galactosidase. J Mol Biol 1969;46:441-446.
    • (1969) J Mol Biol , vol.46 , pp. 441-446
    • Goldberg, M.E.1
  • 9
    • 0015597839 scopus 로고
    • Nucleation, rapid folding, and globular intrachain regions in proteins
    • Wetlaufer DB. Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Natl Acad Sci USA 1973;70:697-701.
    • (1973) Proc Natl Acad Sci USA , vol.70 , pp. 697-701
    • Wetlaufer, D.B.1
  • 10
    • 0019443447 scopus 로고
    • The anatomy and taxonomy of protein structure
    • Richardson JS. The anatomy and taxonomy of protein structure. Adv Protein Chem 1981;34:167-339.
    • (1981) Adv Protein Chem , vol.34 , pp. 167-339
    • Richardson, J.S.1
  • 13
    • 23144463912 scopus 로고    scopus 로고
    • FFAS03: A server for profile-profile sequence alignments
    • Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A. FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Res 2005;33(Web Server issue):W284-8.
    • (2005) Nucleic Acids Res , vol.33 , Issue.WEB SERVER ISSUE
    • Jaroszewski, L.1    Rychlewski, L.2    Li, Z.3    Li, W.4    Godzik, A.5
  • 14
    • 0033997036 scopus 로고    scopus 로고
    • Comparison of sequence profiles. Strategies for structural predictions using sequence information
    • Rychlewski L, Jaroszewski L, Li W, Godzik A. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci 2000;9:232-241.
    • (2000) Protein Sci , vol.9 , pp. 232-241
    • Rychlewski, L.1    Jaroszewski, L.2    Li, W.3    Godzik, A.4
  • 15
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: A simple approach to improve protein structure predictions
    • Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003;19:1015-1018.
    • (2003) Bioinformatics , vol.19 , pp. 1015-1018
    • Ginalski, K.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4
  • 19
    • 0034977013 scopus 로고    scopus 로고
    • A normalized root-mean-square distance for comparing protein three-dimensional structures
    • Carugo O, Pongor S. A normalized root-mean-square distance for comparing protein three-dimensional structures. Protein Sci 2001;10:1470-1473.
    • (2001) Protein Sci , vol.10 , pp. 1470-1473
    • Carugo, O.1    Pongor, S.2
  • 21
    • 0028464982 scopus 로고
    • Parametric and ensemble sequence alignment algorithms
    • Waterman MS. Parametric and ensemble sequence alignment algorithms. Bull Math Biol 1994;56:743-767.
    • (1994) Bull Math Biol , vol.56 , pp. 743-767
    • Waterman, M.S.1
  • 22
    • 0036081436 scopus 로고    scopus 로고
    • In search for more accurate alignments in the twilight zone
    • Jaroszewski L, Li W, Godzik A. In search for more accurate alignments in the twilight zone. Protein Sci 2002;11:1702-1713.
    • (2002) Protein Sci , vol.11 , pp. 1702-1713
    • Jaroszewski, L.1    Li, W.2    Godzik, A.3
  • 23
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
    • (1999) J Mol Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 24
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998;14:846-856.
    • (1998) Bioinformatics , vol.14 , pp. 846-856
    • Karplus, K.1    Barrett, C.2    Hughey, R.3
  • 26
    • 2442449534 scopus 로고    scopus 로고
    • Modeling structurally variable regions in homologous proteins with rosetta
    • Rohl CA, Strauss CE, Chivian D, Baker D. Modeling structurally variable regions in homologous proteins with rosetta. Proteins 2004;55:656-677.
    • (2004) Proteins , vol.55 , pp. 656-677
    • Rohl, C.A.1    Strauss, C.E.2    Chivian, D.3    Baker, D.4
  • 28
    • 0141978673 scopus 로고    scopus 로고
    • Comparative protein structure modeling by iterative alignment, model building and model assessment
    • John B, Sali A. Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res 2003;31:3982-3992.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3982-3992
    • John, B.1    Sali, A.2
  • 29
    • 0037414421 scopus 로고    scopus 로고
    • In silico protein recombination: Enhancing template and sequence alignment selection for comparative protein modelling
    • Contreras-Moreira B, Fitzjohn PW, Bates PA. In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling. J Mol Biol 2003;328:593-608.
    • (2003) J Mol Biol , vol.328 , pp. 593-608
    • Contreras-Moreira, B.1    Fitzjohn, P.W.2    Bates, P.A.3
  • 30
    • 10744220076 scopus 로고    scopus 로고
    • Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling
    • Petrey D, Xiang Z, Tang CL, Xie L, Gimpelev M, Mitros T, Soto CS, Goldsmith-Fischman S, Kernytsky A, et al. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins 2003;Suppl 6:430-435.
    • (2003) Proteins , Issue.SUPPL. 6 , pp. 430-435
    • Petrey, D.1    Xiang, Z.2    Tang, C.L.3    Xie, L.4    Gimpelev, M.5    Mitros, T.6    Soto, C.S.7    Goldsmith-Fischman, S.8    Kernytsky, A.9
  • 31
    • 1842326139 scopus 로고    scopus 로고
    • Bayesian statistical analysis of protein side-chain rotamer preferences
    • Dunbrack RL Jr., Cohen FE. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 1997;6:1661-1681.
    • (1997) Protein Sci , vol.6 , pp. 1661-1681
    • Dunbrack Jr., R.L.1    Cohen, F.E.2
  • 32
    • 0034641749 scopus 로고    scopus 로고
    • Native protein sequences are close to optimal for their structures
    • Kuhlman B, Baker D. Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci USA 2000;97:10383-10388.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 10383-10388
    • Kuhlman, B.1    Baker, D.2
  • 33
    • 0037406075 scopus 로고    scopus 로고
    • Cyclic coordinate descent: A robotics algorithm for protein loop closure
    • Canutescu AA, Dunbrack RL Jr., Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci 2003;12:963-972.
    • (2003) Protein Sci , vol.12 , pp. 963-972
    • Canutescu, A.A.1    Dunbrack Jr., R.L.2
  • 34
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A 1992;89:10915-10919.
    • (1992) Proc Natl Acad Sci U S A , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 36
    • 0038634975 scopus 로고    scopus 로고
    • Improvement of the GenTHREADER method for genomic fold recognition
    • McGuffin LJ, Jones DT. Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 2003;19:874-881.
    • (2003) Bioinformatics , vol.19 , pp. 874-881
    • McGuffin, L.J.1    Jones, D.T.2
  • 37
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • Jones DT. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 1999;287:797-815.
    • (1999) J Mol Biol , vol.287 , pp. 797-815
    • Jones, D.T.1
  • 38
    • 0035967880 scopus 로고    scopus 로고
    • FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
    • 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;310:243-257.
    • (2001) J Mol Biol , vol.310 , pp. 243-257
    • Shi, J.1    Blundell, T.L.2    Mizuguchi, K.3
  • 39
    • 0034595501 scopus 로고    scopus 로고
    • Enhanced genome annotation using structural profiles in the program 3D-PSSM
    • Kelley LA, MacCallum RM, Sternberg MJ. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 2000;299:499-520.
    • (2000) J Mol Biol , vol.299 , pp. 499-520
    • Kelley, L.A.1    MacCallum, R.M.2    Sternberg, M.J.3
  • 40
    • 0033654768 scopus 로고    scopus 로고
    • Hybrid fold recognition: Combining sequence derived properties with evolutionary information
    • Fischer D. Hybrid fold recognition: combining sequence derived properties with evolutionary information. Pac Symp Biocomput 2000:119-130.
    • (2000) Pac Symp Biocomput , pp. 119-130
    • Fischer, D.1
  • 42
    • 0032951163 scopus 로고    scopus 로고
    • Protein structural domain identification
    • Taylor WR. Protein structural domain identification. Protein Eng 1999;12:203-216.
    • (1999) Protein Eng , vol.12 , pp. 203-216
    • Taylor, W.R.1
  • 44
    • 0042622381 scopus 로고    scopus 로고
    • LGA: A method for finding 3D similarities in protein structures
    • Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res 2003;31:3370-3374.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3370-3374
    • Zemla, A.1
  • 45
    • 0036839162 scopus 로고    scopus 로고
    • MAMMOTH (matching molecular models obtained from theory): An automated method for model comparison
    • Ortiz AR, Strauss CE, Olmea O. MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci 2002;11:2606-2621.
    • (2002) Protein Sci , vol.11 , pp. 2606-2621
    • Ortiz, A.R.1    Strauss, C.E.2    Olmea, O.3
  • 46
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.