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Volumn 53, Issue SUPPL. 6, 2003, Pages 457-468

Rosetta Predictions in CASP5: Successes, Failures, and Prospects for Complete Automation

Author keywords

CASP; Fragment insertion; Full atom refinement; Protein structure prediction; ROSETTA

Indexed keywords

AMINO TERMINAL SEQUENCE; AUTOMATION; CARBOXY TERMINAL SEQUENCE; CASP5 TARGET; CLINICAL PROTOCOL; CONFERENCE PAPER; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN STRUCTURE; PROTEIN TARGETING; ROSETTA FRAGMENT INSERTION PROTOCOL; STRUCTURE ANALYSIS;

EID: 10744226366     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10552     Document Type: Conference Paper
Times cited : (160)

References (21)
  • 1
    • 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
  • 2
    • 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 Function, and Genetics 1999;34:82-95.
    • (1999) Proteins Function, and Genetics , 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
  • 3
    • 0032612579 scopus 로고    scopus 로고
    • Ab initio protein structure prediction of CASP III targets using Rosetta
    • Simons KT, Bonneau R, Ruczinski I, Baker D. Ab initio protein structure prediction of CASP III targets using Rosetta. Proteins 1999;Suppl 3:171-176.
    • (1999) Proteins , Issue.SUPPL. 3 , pp. 171-176
    • Simons, K.T.1    Bonneau, R.2    Ruczinski, I.3    Baker, D.4
  • 5
    • 0036073603 scopus 로고    scopus 로고
    • Contact order and ab initio protein structure prediction
    • Bonneau R, Ruczinski I, Tsai J, Baker D. Contact order and ab initio protein structure prediction. Protein Sci 2002;11:1937-1944.
    • (2002) Protein Sci , vol.11 , pp. 1937-1944
    • Bonneau, R.1    Ruczinski, I.2    Tsai, J.3    Baker, D.4
  • 6
    • 0036643499 scopus 로고    scopus 로고
    • Distributions of beta sheets in proteins with application to structure prediction
    • Ruczinski I, Kooperberg C, Bonneau R, Baker D. Distributions of beta sheets in proteins with application to structure prediction. Proteins 2002;48:85-97.
    • (2002) Proteins , vol.48 , pp. 85-97
    • Ruczinski, I.1    Kooperberg, C.2    Bonneau, R.3    Baker, D.4
  • 8
    • 0035789525 scopus 로고    scopus 로고
    • Generation and evaluation of dimension reduced amino acid parameter representations by artificial neural networks
    • Meiler J, Müller M, Zeidler A, Schmäschke F. Generation and evaluation of dimension reduced amino acid parameter representations by artificial neural networks. J Mol Model 2001;7(9):360-369.
    • (2001) J Mol Model , vol.7 , Issue.9 , pp. 360-369
    • Meiler, J.1    Müller, M.2    Zeidler, A.3    Schmäschke, F.4
  • 9
    • 0038675537 scopus 로고    scopus 로고
    • Conserved residue clustering and protein structure prediction
    • Schueler-Furman O, Baker D. Conserved residue clustering and protein structure prediction. Proteins 2003;52:225-235.
    • (2003) Proteins , vol.52 , pp. 225-235
    • Schueler-Furman, O.1    Baker, D.2
  • 10
    • 0036839162 scopus 로고    scopus 로고
    • MAMMOTH (matching molecular models obtained from theory): An automated method for model comparison
    • Ortiz AR, Strauss CEM, Olmea O. MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci 2002;11:2606-2611.
    • (2002) Protein Sci , vol.11 , pp. 2606-2611
    • Ortiz, A.R.1    Strauss, C.E.M.2    Olmea, O.3
  • 12
    • 0034780030 scopus 로고    scopus 로고
    • Pcons: A neural-network-based consensus predictor that improves fold recognition
    • Lundstroem J, Rychlewski L, Bujnicki J, Elofsson A. Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci 2001;10:2354-2362.
    • (2001) Protein Sci , vol.10 , pp. 2354-2362
    • Lundstroem, J.1    Rychlewski, L.2    Bujnicki, J.3    Elofsson, A.4
  • 13
    • 0035314042 scopus 로고    scopus 로고
    • Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation
    • Bonneau R, Strauss CEM, Baker D. Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation. Proteins 2001;43:1-11.
    • (2001) Proteins , vol.43 , pp. 1-11
    • Bonneau, R.1    Strauss, C.E.M.2    Baker, D.3
  • 14
    • 0038008976 scopus 로고    scopus 로고
    • An impared protein decoy set for testing energy functions for protein structure prediction
    • Tsai J, Bonneau R, Rohl C, Baker D. An impared protein decoy set for testing energy functions for protein structure prediction. Proteins 2003;53:76-87.
    • (2003) Proteins , vol.53 , pp. 76-87
    • Tsai, J.1    Bonneau, R.2    Rohl, C.3    Baker, D.4
  • 15
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol 1981;147:195-197.
    • (1981) J Mol Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 16
    • 1842326139 scopus 로고    scopus 로고
    • Bayesian statistical analysis of protein side-chain rotamer preferences
    • Dunbrack RL, 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, R.L.1    Cohen, F.E.2
  • 17
    • 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
  • 18
    • 0035703310 scopus 로고    scopus 로고
    • Processing and evaluation of predictions in CASP4
    • Zemla A, Venclovas C, Moult J, Fidelis K. Processing and evaluation of predictions in CASP4. Proteins 2001;Suppl 5:13-21
    • (2001) Proteins , Issue.SUPPL. 5 , pp. 13-21
    • Zemla, A.1    Venclovas, C.2    Moult, J.3    Fidelis, K.4
  • 19
    • 0033670439 scopus 로고    scopus 로고
    • MaxSub: An automated measure for the assessment of protein structure prediction quality
    • Siew N, Elofsson A, Rychlewski L, Fischer D. MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 2000;16:776-785.
    • (2000) Bioinformatics , vol.16 , pp. 776-785
    • Siew, N.1    Elofsson, A.2    Rychlewski, L.3    Fischer, D.4
  • 20
    • 0242338293 scopus 로고    scopus 로고
    • Modeling structurally variable regions in homologous proteins with Rosetta
    • In Press
    • Rohl CA, Strauss CEM, Chivian D, Baker D. Modeling structurally variable regions in homologous proteins with Rosetta. Proteins 2003. In Press.
    • (2003) Proteins
    • Rohl, C.A.1    Strauss, C.E.M.2    Chivian, D.3    Baker, D.4
  • 21
    • 0142027795 scopus 로고    scopus 로고
    • Coupled prediction of protein secondary and tertiary structure
    • In Press
    • Meiler J, Baker D. Coupled prediction of protein secondary and tertiary structure. PNAS 2003. In Press.
    • (2003) PNAS
    • Meiler, J.1    Baker, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.