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Volumn 69, Issue SUPPL. 8, 2007, Pages 90-97

Analysis of TASSER-based CASP7 protein structure prediction results

Author keywords

3D jury; Ab initio structure prediction; Fold recognition; MetaTASSER; PROSPECTOR_3; SP 3; SPARKS; TASSER; Template based modeling

Indexed keywords

AMINO ACID SEQUENCE; CONFERENCE PAPER; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

EID: 36749095600     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21649     Document Type: Conference Paper
Times cited : (60)

References (33)
  • 1
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker D, Sali A. Protein structure prediction and structural genomics. Science 2001;294:93-96.
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 2
    • 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
  • 3
    • 0034060287 scopus 로고    scopus 로고
    • Structural genomics and its importance for gene function analysis
    • Skolnick J, Fetrow J, Kolinski A. Structural genomics and its importance for gene function analysis. Nat Biotechnol 2000;18:283-287.
    • (2000) Nat Biotechnol , vol.18 , pp. 283-287
    • Skolnick, J.1    Fetrow, J.2    Kolinski, A.3
  • 4
    • 2442676589 scopus 로고    scopus 로고
    • Automated structure prediction of weakly homologous proteins on genomic scale
    • Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on genomic scale. Proc Natl Acad Sci USA 2004;101:7594-7599.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 7594-7599
    • Zhang, Y.1    Skolnick, J.2
  • 6
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992;358:86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 8
    • 0028047892 scopus 로고
    • Sequence alignment and penalty choice. Review of concepts, case studies and implications
    • Vingron M, Waterman MS. Sequence alignment and penalty choice. Review of concepts, case studies and implications. J Mol Biol 1994;235:1-12.
    • (1994) J Mol Biol , vol.235 , pp. 1-12
    • Vingron, M.1    Waterman, M.S.2
  • 10
    • 0037271276 scopus 로고    scopus 로고
    • Fold recognition methods
    • Godzik A. Fold recognition methods. Methods Biochem Anal 2003;44:525-546.
    • (2003) Methods Biochem Anal , vol.44 , pp. 525-546
    • Godzik, A.1
  • 11
    • 0033846832 scopus 로고    scopus 로고
    • Improving the quality of twilight-zone alignment
    • Jaroszewski L, Rychlewski L, Godzik A. Improving the quality of twilight-zone alignment. Protein Sci 2000;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
    • Jaroszewski L, Rychlewski 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
    • Jaroszewski, L.1    Rychlewski, L.2    Li, W.3    Godzik, A.4
  • 13
    • 0034328688 scopus 로고    scopus 로고
    • 3D-1D threading methods for protein fold recognition
    • David R, Korenberg MJ, Hunter IW. 3D-1D threading methods for protein fold recognition. Pharmacogenomics 2000;1:445-455.
    • (2000) Pharmacogenomics , vol.1 , pp. 445-455
    • David, R.1    Korenberg, M.J.2    Hunter, I.W.3
  • 14
    • 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
  • 15
    • 0034780030 scopus 로고    scopus 로고
    • Pcons: A neural-network-based consensus predictor that improves fold recognition
    • Lundsröm J, Rychlewski L, Bunnicki 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
    • Lundsröm, J.1    Rychlewski, L.2    Bunnicki, J.3    Elofsson, A.4
  • 16
    • 0242299169 scopus 로고    scopus 로고
    • Automatic consensus-based fold recognition using Peons, Pro Q, and Pmodeller
    • Wallner B, Fang H, Elosson A. Automatic consensus-based fold recognition using Peons, Pro Q, and Pmodeller. Proteins: Struct Funct Genet Suppl 2003;6:534-541.
    • (2003) Proteins: Struct Funct Genet Suppl , vol.6 , pp. 534-541
    • Wallner, B.1    Fang, H.2    Elosson, A.3
  • 17
    • 0037624841 scopus 로고    scopus 로고
    • 3D-SHOTGUN: A novel, cooperative, fold-recognition meta-predictor
    • Fischer D. 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor. Proteins 2003;51:434-441.
    • (2003) Proteins , vol.51 , pp. 434-441
    • Fischer, D.1
  • 18
    • 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
    • 2442676589 scopus 로고    scopus 로고
    • Automated structure prediction of weakly homologous proteins on genomic scale
    • Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on genomic scale. Proc Natl Acad Sci USA 2004;101:7594-7599.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 7594-7599
    • Zhang, Y.1    Skolnick, J.2
  • 20
    • 7444236378 scopus 로고    scopus 로고
    • Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation
    • Qian B, Ortiz AR, Baker D. Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. Proc Natl Acad Sci USA 2004;101:15346-15351.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 15346-15351
    • Qian, B.1    Ortiz, A.R.2    Baker, D.3
  • 21
    • 33645792604 scopus 로고    scopus 로고
    • Physically realistic homology models built with ROSETTA can be more accurate than their templates
    • Misura KM, Chivian D, Rohl CA, Kim DE, Baker D. Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc Natl Acad Sci USA 2004;103:5361-6366.
    • (2004) Proc Natl Acad Sci USA , vol.103 , pp. 5361-6366
    • Misura, K.M.1    Chivian, D.2    Rohl, C.A.3    Kim, D.E.4    Baker, D.5
  • 22
    • 33747854222 scopus 로고    scopus 로고
    • Developing a move-set for protein model refinement
    • Offman MN, Fitzjohn PW, Bates PA. Developing a move-set for protein model refinement. Bioinformatics 2006;22:1838-1845.
    • (2006) Bioinformatics , vol.22 , pp. 1838-1845
    • Offman, M.N.1    Fitzjohn, P.W.2    Bates, P.A.3
  • 23
    • 13844291273 scopus 로고    scopus 로고
    • Protein refinement: A new challenge for CASP in its 10th anniversary
    • Valencia A. Protein refinement: a new challenge for CASP in its 10th anniversary. Bioinformatics 2005;21:277.
    • (2005) Bioinformatics , vol.21 , pp. 277
    • Valencia, A.1
  • 24
    • 9144244232 scopus 로고    scopus 로고
    • Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 2004;32:D217-D222.
    • Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 2004;32:D217-D222.
  • 25
    • 30344488120 scopus 로고    scopus 로고
    • TASSER: An automated method for the prediction of protein tertiary structures in CASP6
    • Zhang Y, Arakaki A, Skolnick J. TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins 2005;61 (Suppl 7):91-98.
    • (2005) Proteins , vol.61 , Issue.SUPPL. 7 , pp. 91-98
    • Zhang, Y.1    Arakaki, A.2    Skolnick, J.3
  • 26
    • 3142764482 scopus 로고    scopus 로고
    • Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm
    • Skolnick J, Kihara D, Zhang Y. Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm. Proteins 2004;56:502-518.
    • (2004) Proteins , vol.56 , pp. 502-518
    • Skolnick, J.1    Kihara, D.2    Zhang, Y.3
  • 27
    • 2542631929 scopus 로고    scopus 로고
    • Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition
    • Zhou H, Zhou Y. Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins 2004;55:1005-1013.
    • (2004) Proteins , vol.55 , pp. 1005-1013
    • Zhou, H.1    Zhou, Y.2
  • 28
    • 11344292852 scopus 로고    scopus 로고
    • Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments
    • Zhou H, Zhou Y. Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins 2005;58:321-328.
    • (2005) Proteins , vol.58 , pp. 321-328
    • Zhou, H.1    Zhou, Y.2
  • 29
    • 30344456694 scopus 로고    scopus 로고
    • 3 servers in CASP 6. Proteins (Suppl CASP Issue) 2005; (Suppl 7):152-156.
    • 3 servers in CASP 6. Proteins (Suppl CASP Issue) 2005; (Suppl 7):152-156.
  • 30
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: 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 2005;33:2302-2309.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 31
    • 10344232638 scopus 로고    scopus 로고
    • A scoring function for the automated assessment of protein structure template quality
    • Zhang Y, Skolnick J. A scoring function for the automated assessment of protein structure template quality. Proteins 2004;57:702-710.
    • (2004) Proteins , vol.57 , pp. 702-710
    • Zhang, Y.1    Skolnick, J.2
  • 32
    • 0036681386 scopus 로고    scopus 로고
    • Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding
    • Zhang Y, Kihara D, Skolnick J. Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins 2002;48:192-201.
    • (2002) Proteins , vol.48 , pp. 192-201
    • Zhang, Y.1    Kihara, D.2    Skolnick, J.3
  • 33
    • 1942519275 scopus 로고    scopus 로고
    • SPICKER: A clustering approach to identify near-native protein fold
    • Zhang Y, Skolnick J. SPICKER: a clustering approach to identify near-native protein fold. J Comput Chem 2004;25:865-871.
    • (2004) J Comput Chem , vol.25 , pp. 865-871
    • Zhang, Y.1    Skolnick, J.2


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