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Volumn 32, Issue WEB SERVER ISS., 2004, Pages

Protein structure prediction and analysis using the Robetta server

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; COMPUTER PROGRAM; COMPUTER SYSTEM; INFORMATION SYSTEM; INTERMETHOD COMPARISON; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

EID: 3242887695     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh468     Document Type: Article
Times cited : (1636)

References (38)
  • 1
    • 0034501067 scopus 로고    scopus 로고
    • De novo protein structure determination using sparse NMR data
    • Bowers,P.M., Strauss,C.E. and Baker,D. (2000) De novo protein structure determination using sparse NMR data. J. Biomol. NMR, 18, 311-318.
    • (2000) J. Biomol. NMR , vol.18 , pp. 311-318
    • Bowers, P.M.1    Strauss, C.E.2    Baker, D.3
  • 2
    • 0037139549 scopus 로고    scopus 로고
    • De novo determination of protein backbone structure from residual dipolar couplings using Rosetta
    • Rohl,C.A. and Baker,D. (2002) De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. J. Am. Chem. Soc., 124, 2723-2729.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 2723-2729
    • Rohl, C.A.1    Baker, D.2
  • 3
    • 0346103679 scopus 로고    scopus 로고
    • Rapid protein fold determination using unassigned NMR data
    • Meiler,J. and Baker,D. (2003) Rapid protein fold determination using unassigned NMR data. Proc. Natl Acad. Sci. USA, 100, 15404-15409.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 15404-15409
    • Meiler, J.1    Baker, D.2
  • 4
    • 3242879771 scopus 로고    scopus 로고
    • Computational alanine scanning of protein-protein interfaces
    • Kortemme,T., Kim,D.E. and Baker,D. (2004) Computational alanine scanning of protein-protein interfaces. Sci. STKE, 2004, p12.
    • (2004) Sci. STKE , vol.2004 , pp. 12
    • Kortemme, T.1    Kim, D.E.2    Baker, D.3
  • 5
    • 0037195144 scopus 로고    scopus 로고
    • A simple physical model for binding energy hot spots in protein-protein complexes
    • Kortemme,T. and Baker,D. (2002) A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl Acad. Sci. USA, 99, 14116-14121.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 14116-14121
    • Kortemme, T.1    Baker, D.2
  • 8
    • 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,K.T., Ruczinski,I., Kooperberg,C., Fox,B.A., Bystroff,C. and Baker,D. (1999) Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins, 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
  • 9
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons,K.T., Kooperberg,C., Huang,E. and Baker,D. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol., 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
  • 11
    • 0033846832 scopus 로고    scopus 로고
    • Improving the quality of twilight-zone alignments
    • Jaroszewski,L., Rychlewski,L. and Godzik,A. (2000) Improving the quality of twilight-zone alignments. Protein Sci., 9, 1487-1496.
    • (2000) Protein Sci. , vol.9 , pp. 1487-1496
    • Jaroszewski, L.1    Rychlewski, L.2    Godzik, A.3
  • 12
    • 0033997036 scopus 로고    scopus 로고
    • Comparison of sequence profiles. Strategies for structural predictions using sequence information
    • Rychlewski,L., Jaroszewski,L., Li,W. and Godzik,A. (2000) Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci., 9, 232-241.
    • (2000) Protein Sci. , vol.9 , pp. 232-241
    • Rychlewski, L.1    Jaroszewski, L.2    Li, W.3    Godzik, A.4
  • 13
    • 0041620404 scopus 로고    scopus 로고
    • Detection of reliable and unexpected protein fold predictions using 3D-Jury
    • Ginalski,K. and Rychlewski,L. (2003) Detection of reliable and unexpected protein fold predictions using 3D-Jury. Nucleic Acids Res., 31, 3291-3292.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3291-3292
    • Ginalski, K.1    Rychlewski, L.2
  • 14
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: A simple approach to improve protein structure predictions
    • Ginalski,K., Elofsson,A., Fischer,D. and Rychlewski,L. (2003) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics, 19, 1015-1018.
    • (2003) Bioinformatics , vol.19 , pp. 1015-1018
    • Ginalski, K.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4
  • 16
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 17
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones,D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 18
    • 0033753811 scopus 로고    scopus 로고
    • Domain size distributions can predict domain boundaries
    • Wheelan,S.J., Marchler-Bauer,A. and Bryant,S.H. (2000) Domain size distributions can predict domain boundaries. Bioinformatics, 16, 613-618.
    • (2000) Bioinformatics , vol.16 , pp. 613-618
    • Wheelan, S.J.1    Marchler-Bauer, A.2    Bryant, S.H.3
  • 19
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 20
    • 2442449534 scopus 로고    scopus 로고
    • Modeling structurally variable regions in homologous proteins with Rosetta
    • Rohl,C.A., Strauss,C.E., Chivian,D. and Baker,D. (2004) Modeling structurally variable regions in homologous proteins with Rosetta. Proteins, 55, 656-677.
    • (2004) Proteins , vol.55 , pp. 656-677
    • Rohl, C.A.1    Strauss, C.E.2    Chivian, D.3    Baker, D.4
  • 21
    • 0036839162 scopus 로고    scopus 로고
    • MAMMOTH (matching molecular models obtained from theory): An automated method for model comparison
    • Ortiz,A.R., Strauss,C.E. and Olmea,O. (2002) MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci., 11, 2606-2621.
    • (2002) Protein Sci. , vol.11 , pp. 2606-2621
    • Ortiz, A.R.1    Strauss, C.E.2    Olmea, O.3
  • 22
    • 0033670439 scopus 로고    scopus 로고
    • MaxSub: An automated measure for the assessment of protein structure prediction quality
    • Siew,N., Elofsson,A., Rychlewski,L. and Fischer,D. (2000) MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics, 16, 776-785.
    • (2000) Bioinformatics , vol.16 , pp. 776-785
    • Siew, N.1    Elofsson, A.2    Rychlewski, L.3    Fischer, D.4
  • 23
    • 0034641749 scopus 로고    scopus 로고
    • Native protein sequences are close to optimal for their structures
    • Kuhlman,B. and Baker,D. (2000) Native protein sequences are close to optimal for their structures. Proc. Natl Acad. Sci. USA, 97, 10383-10388.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 10383-10388
    • Kuhlman, B.1    Baker, D.2
  • 24
    • 1842326139 scopus 로고    scopus 로고
    • Bayesian statistical analysis of protein side-chain rotamer preferences
    • Dunbrack,R.L.,Jr and Cohen,F.E. (1997) Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci., 6, 1661-1681.
    • (1997) Protein Sci. , vol.6 , pp. 1661-1681
    • Dunbrack Jr., R.L.1    Cohen, F.E.2
  • 25
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • Krogh,A., Larsson,B., von Heijne,G. and Sonnhammer,E.L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol., 305, 567-580.
    • (2001) J. Mol. Biol. , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.4
  • 27
    • 0029901640 scopus 로고    scopus 로고
    • Analysis of compositionally biased regions in sequence databases
    • Wootton,J.C. and Federhen,S. (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol., 266, 554-571.
    • (1996) Methods Enzymol. , vol.266 , pp. 554-571
    • Wootton, J.C.1    Federhen, S.2
  • 28
    • 0026356891 scopus 로고
    • Predicting coiled coils from protein sequences
    • Lupas,A., Van Dyke,M. and Stock,J. (1991) Predicting coiled coils from protein sequences. Science, 252, 1162-1164.
    • (1991) Science , vol.252 , pp. 1162-1164
    • Lupas, A.1    Van Dyke, M.2    Stock, J.3
  • 29
    • 0242362157 scopus 로고    scopus 로고
    • Prediction of disordered regions in proteins from position specific score matrices
    • Jones,D.T. and Ward,J.J. (2003) Prediction of disordered regions in proteins from position specific score matrices. Proteins, 53 (Suppl. 6), 573-578.
    • (2003) Proteins , vol.53 , Issue.SUPPL. 6 , pp. 573-578
    • Jones, D.T.1    Ward, J.J.2
  • 31
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • Karplus,K., Barrett,C. and Hughey,R. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846-856.
    • (1998) Bioinformatics , vol.14 , pp. 846-856
    • Karplus, K.1    Barrett, C.2    Hughey, R.3
  • 32
    • 0142027795 scopus 로고    scopus 로고
    • Coupled prediction of protein secondary and tertiary structure
    • Meiler,J. and Baker,D. (2003) Coupled prediction of protein secondary and tertiary structure. Proc. Natl Acad. Sci. USA, 100, 12105-12110.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 12105-12110
    • Meiler, J.1    Baker, D.2
  • 33
    • 0028502226 scopus 로고
    • The evolution and recognition of protein sequence repeats
    • Heringa,J. (1994) The evolution and recognition of protein sequence repeats. Comput. Chem., 18, 233-243.
    • (1994) Comput. Chem. , vol.18 , pp. 233-243
    • Heringa, J.1
  • 34
    • 0027491666 scopus 로고
    • A method to recognize distant repeats in protein sequences
    • Heringa,J. and Argos,P. (1993) A method to recognize distant repeats in protein sequences. Proteins, 17, 391-411.
    • (1993) Proteins , vol.17 , pp. 391-411
    • Heringa, J.1    Argos, P.2
  • 35
    • 0242330720 scopus 로고    scopus 로고
    • LiveBench-6:large-scale automated evaluation of protein structure prediction servers
    • Rychlewski,L., Fischer,D. and Elofsson,A. (2003) LiveBench-6: large-scale automated evaluation of protein structure prediction servers. Proteins, 53 (Suppl. 6), 542-547.
    • (2003) Proteins , vol.53 , Issue.SUPPL. 6 , pp. 542-547
    • Rychlewski, L.1    Fischer, D.2    Elofsson, A.3
  • 36
  • 37
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray,J.J., Moughon,S., Wang,C., Schueler-Furman,O., Kuhlman,B., Rohl,C.A. and Baker,D. (2003) Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol., 331, 281-299.
    • (2003) J. Mol. Biol. , vol.331 , pp. 281-299
    • Gray, J.J.1    Moughon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.A.6    Baker, D.7


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