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Volumn 7, Issue 11, 2012, Pages

eThread: A Highly Optimized Machine Learning-Based Approach to Meta-Threading and the Modeling of Protein Tertiary Structures

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; AUTOMATION; CLASSIFIER; INTERMETHOD COMPARISON; MACHINE LEARNING; MOLECULAR MODEL; PREDICTION; PROCESS DEVELOPMENT; PROCESS OPTIMIZATION; PROTEIN TERTIARY STRUCTURE; QUALITY CONTROL;

EID: 84869842288     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0050200     Document Type: Article
Times cited : (33)

References (80)
  • 1
    • 79551651006 scopus 로고    scopus 로고
    • Advances in whole genome sequencing technology
    • Zhao J, Grant SF, (2011) Advances in whole genome sequencing technology. Curr Pharm Biotechnol 12: 293-305.
    • (2011) Curr Pharm Biotechnol , vol.12 , pp. 293-305
    • Zhao, J.1    Grant, S.F.2
  • 3
    • 74549221383 scopus 로고    scopus 로고
    • Annotation error in public databases: misannotation of molecular function in enzyme superfamilies
    • Schnoes AM, Brown SD, Dodevski I, Babbitt PC, (2009) Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol 5: e1000605.
    • (2009) PLoS Comput Biol , vol.5
    • Schnoes, A.M.1    Brown, S.D.2    Dodevski, I.3    Babbitt, P.C.4
  • 4
    • 67449108422 scopus 로고    scopus 로고
    • FINDSITE: a combined evolution/structure-based approach to protein function prediction
    • Skolnick J, Brylinski M, (2009) FINDSITE: a combined evolution/structure-based approach to protein function prediction. Brief Bioinform 10: 378-391.
    • (2009) Brief Bioinform , vol.10 , pp. 378-391
    • Skolnick, J.1    Brylinski, M.2
  • 5
    • 77954065271 scopus 로고    scopus 로고
    • I-TASSER: a unified platform for automated protein structure and function prediction
    • Roy A, Kucukural A, Zhang Y, (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5: 725-738.
    • (2010) Nat Protoc , vol.5 , pp. 725-738
    • Roy, A.1    Kucukural, A.2    Zhang, Y.3
  • 6
    • 38349100452 scopus 로고    scopus 로고
    • A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
    • Brylinski M, Skolnick J, (2008) A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci U S A 105: 129-134.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 129-134
    • Brylinski, M.1    Skolnick, J.2
  • 7
    • 74249102742 scopus 로고    scopus 로고
    • Protein-binding site prediction based on three-dimensional protein modeling
    • Oh M, Joo K, Lee J, (2009) Protein-binding site prediction based on three-dimensional protein modeling. Proteins 77Suppl 9: 152-156.
    • (2009) Proteins , vol.77 , pp. 152-156
    • Oh, M.1    Joo, K.2    Lee, J.3
  • 8
    • 74249093489 scopus 로고    scopus 로고
    • Prediction of ligand binding sites using homologous structures and conservation at CASP8
    • Wass MN, Sternberg MJ, (2009) Prediction of ligand binding sites using homologous structures and conservation at CASP8. Proteins 77Suppl 9: 147-151.
    • (2009) Proteins , vol.77 , pp. 147-151
    • Wass, M.N.1    Sternberg, M.J.2
  • 9
    • 64549115839 scopus 로고    scopus 로고
    • Protein structure prediction: when is it useful?
    • Zhang Y, (2009) Protein structure prediction: when is it useful? Curr Opin Struct Biol 19: 145-155.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 145-155
    • Zhang, Y.1
  • 10
    • 29144526714 scopus 로고    scopus 로고
    • Protein structure prediction: inroads to biology
    • Petrey D, Honig B, (2005) Protein structure prediction: inroads to biology. Mol Cell 20: 811-819.
    • (2005) Mol Cell , vol.20 , pp. 811-819
    • Petrey, D.1    Honig, B.2
  • 11
    • 80054685109 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP)-round IX
    • Moult J, Fidelis K, Kryshtafovych A, Tramontano A, (2011) Critical assessment of methods of protein structure prediction (CASP)-round IX. Proteins 79Suppl 10: 1-5.
    • (2011) Proteins , vol.79 , pp. 1-5
    • Moult, J.1    Fidelis, K.2    Kryshtafovych, A.3    Tramontano, A.4
  • 12
    • 34250851687 scopus 로고    scopus 로고
    • LOMETS: a local meta-threading-server for protein structure prediction
    • Wu S, Zhang Y, (2007) LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res 35: 3375-3382.
    • (2007) Nucleic Acids Res , vol.35 , pp. 3375-3382
    • Wu, S.1    Zhang, Y.2
  • 13
    • 84862225232 scopus 로고    scopus 로고
    • Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field
    • Xu D, Zhang Y (2012) Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins.
    • (2012) Proteins
    • Xu, D.1    Zhang, Y.2
  • 15
    • 84856489442 scopus 로고    scopus 로고
    • HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
    • Remmert M, Biegert A, Hauser A, Soding J, (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods 9: 173-175.
    • (2012) Nat Methods , vol.9 , pp. 173-175
    • Remmert, M.1    Biegert, A.2    Hauser, A.3    Soding, J.4
  • 16
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 17
    • 79959564695 scopus 로고    scopus 로고
    • The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction
    • Roche DB, Buenavista MT, Tetchner SJ, McGuffin LJ, (2011) The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction. Nucleic Acids Res 39: W171-176.
    • (2011) Nucleic Acids Res , vol.39
    • Roche, D.B.1    Buenavista, M.T.2    Tetchner, S.J.3    McGuffin, L.J.4
  • 18
    • 79960394811 scopus 로고    scopus 로고
    • Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates
    • Yang Y, Faraggi E, Zhao H, Zhou Y, (2011) Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates. Bioinformatics 27: 2076-2082.
    • (2011) Bioinformatics , vol.27 , pp. 2076-2082
    • Yang, Y.1    Faraggi, E.2    Zhao, H.3    Zhou, Y.4
  • 19
    • 77954196482 scopus 로고    scopus 로고
    • Low-homology protein threading
    • Peng J, Xu J, (2010) Low-homology protein threading. Bioinformatics 26: i294-300.
    • (2010) Bioinformatics , vol.26
    • Peng, J.1    Xu, J.2
  • 20
    • 74249119329 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction - Round VIII
    • Moult J, Fidelis K, Kryshtafovych A, Rost B, Tramontano A, (2009) Critical assessment of methods of protein structure prediction- Round VIII. Proteins 77Suppl 9: 1-4.
    • (2009) Proteins , vol.77 , pp. 1-4
    • Moult, J.1    Fidelis, K.2    Kryshtafovych, A.3    Rost, B.4    Tramontano, A.5
  • 21
    • 0034780030 scopus 로고    scopus 로고
    • Pcons: a neural-network-based consensus predictor that improves fold recognition
    • Lundstrom J, Rychlewski L, Bujnicki J, Elofsson A, (2001) Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci 10: 2354-2362.
    • (2001) Protein Sci , vol.10 , pp. 2354-2362
    • Lundstrom, J.1    Rychlewski, L.2    Bujnicki, J.3    Elofsson, A.4
  • 22
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell TL, (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234: 779-815.
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 23
    • 33845365051 scopus 로고    scopus 로고
    • TASSER-Lite: an automated tool for protein comparative modeling
    • Pandit SB, Zhang Y, Skolnick J, (2006) TASSER-Lite: an automated tool for protein comparative modeling. Biophys J 91: 4180-4190.
    • (2006) Biophys J , vol.91 , pp. 4180-4190
    • Pandit, S.B.1    Zhang, Y.2    Skolnick, J.3
  • 24
    • 30344456694 scopus 로고    scopus 로고
    • SPARKS 2 and SP3 servers in CASP6
    • Zhou H, Zhou Y, (2005) SPARKS 2 and SP3 servers in CASP6. Proteins 61Suppl 7: 152-156.
    • (2005) Proteins , vol.61 , pp. 152-156
    • Zhou, H.1    Zhou, Y.2
  • 25
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: a protein sequence culling server
    • Wang G, Dunbrack RL Jr, (2003) PISCES: a protein sequence culling server. Bioinformatics 19: 1589-1591.
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 26
    • 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, (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 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
  • 27
    • 0033977581 scopus 로고    scopus 로고
    • The ASTRAL compendium for protein structure and sequence analysis
    • Brenner SE, Koehl P, Levitt M, (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res 28: 254-256.
    • (2000) Nucleic Acids Res , vol.28 , pp. 254-256
    • Brenner, S.E.1    Koehl, P.2    Levitt, M.3
  • 28
    • 62649147821 scopus 로고    scopus 로고
    • Sequence context-specific profiles for homology searching
    • Biegert A, Soding J, (2009) Sequence context-specific profiles for homology searching. Proc Natl Acad Sci U S A 106: 3770-3775.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 3770-3775
    • Biegert, A.1    Soding, J.2
  • 29
    • 0037423702 scopus 로고    scopus 로고
    • COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance
    • Sadreyev R, Grishin N, (2003) COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol 326: 317-336.
    • (2003) J Mol Biol , vol.326 , pp. 317-336
    • Sadreyev, R.1    Grishin, N.2
  • 30
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Soding J, (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21: 951-960.
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Soding, J.1
  • 31
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy SR, (1998) Profile hidden Markov models. Bioinformatics 14: 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 32
    • 0030093114 scopus 로고    scopus 로고
    • A flexible motif search technique based on generalized profiles
    • Bucher P, Karplus K, Moeri N, Hofmann K, (1996) A flexible motif search technique based on generalized profiles. Comput Chem 20: 3-23.
    • (1996) Comput Chem , vol.20 , pp. 3-23
    • Bucher, P.1    Karplus, K.2    Moeri, N.3    Hofmann, K.4
  • 33
    • 67649887151 scopus 로고    scopus 로고
    • pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination
    • Lobley A, Sadowski MI, Jones DT, (2009) pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination. Bioinformatics 25: 1761-1767.
    • (2009) Bioinformatics , vol.25 , pp. 1761-1767
    • Lobley, A.1    Sadowski, M.I.2    Jones, D.T.3
  • 34
    • 0029887381 scopus 로고    scopus 로고
    • Hidden Markov models for sequence analysis: extension and analysis of the basic method
    • Hughey R, Krogh A, (1996) Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput Appl Biosci 12: 95-107.
    • (1996) Comput Appl Biosci , vol.12 , pp. 95-107
    • Hughey, R.1    Krogh, A.2
  • 35
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones DT, Taylor WR, Thornton JM, (1992) A new approach to protein fold recognition. Nature 358: 86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 37
    • 10344232638 scopus 로고    scopus 로고
    • Scoring function for automated assessment of protein structure template quality
    • Zhang Y, Skolnick J, (2004) Scoring function for automated assessment of protein structure template quality. Proteins 57: 702-710.
    • (2004) Proteins , vol.57 , pp. 702-710
    • Zhang, Y.1    Skolnick, J.2
  • 38
    • 58649097284 scopus 로고    scopus 로고
    • Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score
    • Pandit SB, Skolnick J, (2008) Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. BMC Bioinformatics 9: 531.
    • (2008) BMC Bioinformatics , vol.9 , pp. 531
    • Pandit, S.B.1    Skolnick, J.2
  • 39
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman SB, Wunsch CD, (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-453.
    • (1970) J Mol Biol , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 40
    • 0030983768 scopus 로고    scopus 로고
    • Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?
    • Skolnick J, Jaroszewski L, Kolinski A, Godzik A, (1997) Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci 6: 676-688.
    • (1997) Protein Sci , vol.6 , pp. 676-688
    • Skolnick, J.1    Jaroszewski, L.2    Kolinski, A.3    Godzik, A.4
  • 41
    • 44449124693 scopus 로고    scopus 로고
    • Fast procedure for reconstruction of full-atom protein models from reduced representations
    • Rotkiewicz P, Skolnick J, (2008) Fast procedure for reconstruction of full-atom protein models from reduced representations. J Comput Chem 29: 1460-1465.
    • (2008) J Comput Chem , vol.29 , pp. 1460-1465
    • Rotkiewicz, P.1    Skolnick, J.2
  • 42
    • 0041784950 scopus 로고    scopus 로고
    • All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
    • MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, et al. (1998) All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. J Phys Chem B 102: 3586-3616.
    • (1998) J Phys Chem B , vol.102 , pp. 3586-3616
    • MacKerell, A.D.1    Bashford, D.2    Bellott, M.3    Dunbrack, R.L.4    Evanseck, J.D.5
  • 43
    • 0035838974 scopus 로고    scopus 로고
    • Extending the accuracy limits of prediction for side-chain conformations
    • Xiang Z, Honig B, (2001) Extending the accuracy limits of prediction for side-chain conformations. J Mol Biol 311: 421-430.
    • (2001) J Mol Biol , vol.311 , pp. 421-430
    • Xiang, Z.1    Honig, B.2
  • 45
    • 1642534609 scopus 로고    scopus 로고
    • An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state
    • Zhang C, Liu S, Zhou H, Zhou Y, (2004) An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci 13: 400-411.
    • (2004) Protein Sci , vol.13 , pp. 400-411
    • Zhang, C.1    Liu, S.2    Zhou, H.3    Zhou, Y.4
  • 46
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT, (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
  • 47
    • 1942519275 scopus 로고    scopus 로고
    • SPICKER: a clustering approach to identify near-native protein folds
    • Zhang Y, Skolnick J, (2004) SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 25: 865-871.
    • (2004) J Comput Chem , vol.25 , pp. 865-871
    • Zhang, Y.1    Skolnick, J.2
  • 48
    • 84862276163 scopus 로고    scopus 로고
    • Further evidence for the likely completeness of the library of solved single domain protein structures
    • Skolnick J, Zhou H, Brylinski M, (2012) Further evidence for the likely completeness of the library of solved single domain protein structures. J Phys Chem B 116: 6654-6664.
    • (2012) J Phys Chem B , vol.116 , pp. 6654-6664
    • Skolnick, J.1    Zhou, H.2    Brylinski, M.3
  • 49
    • 16644386061 scopus 로고    scopus 로고
    • Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins
    • Zhang Y, Skolnick J, (2004) Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophys J 87: 2647-2655.
    • (2004) Biophys J , vol.87 , pp. 2647-2655
    • Zhang, Y.1    Skolnick, J.2
  • 50
    • 0033931867 scopus 로고    scopus 로고
    • Assessing the accuracy of prediction algorithms for classification: an overview
    • Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H, (2000) Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16: 412-424.
    • (2000) Bioinformatics , vol.16 , pp. 412-424
    • Baldi, P.1    Brunak, S.2    Chauvin, Y.3    Andersen, C.A.4    Nielsen, H.5
  • 52
    • 34247247779 scopus 로고    scopus 로고
    • Improved residue contact prediction using support vector machines and a large feature set
    • Cheng J, Baldi P, (2007) Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics 8: 113.
    • (2007) BMC Bioinformatics , vol.8 , pp. 113
    • Cheng, J.1    Baldi, P.2
  • 53
    • 62849113729 scopus 로고    scopus 로고
    • SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs
    • Randall A, Baldi P, (2008) SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs. BMC Struct Biol 8: 52.
    • (2008) BMC Struct Biol , vol.8 , pp. 52
    • Randall, A.1    Baldi, P.2
  • 54
    • 79958078892 scopus 로고    scopus 로고
    • APOLLO: a quality assessment service for single and multiple protein models
    • Wang Z, Eickholt J, Cheng J, (2011) APOLLO: a quality assessment service for single and multiple protein models. Bioinformatics 27: 1715-1716.
    • (2011) Bioinformatics , vol.27 , pp. 1715-1716
    • Wang, Z.1    Eickholt, J.2    Cheng, J.3
  • 55
    • 0042622381 scopus 로고    scopus 로고
    • LGA: A method for finding 3D similarities in protein structures
    • Zemla A, (2003) LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res 31: 3370-3374.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3370-3374
    • Zemla, A.1
  • 56
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch W, (1976) A solution for the best rotation to relate two sets of vectors. Acta Cryst 32: 922-923.
    • (1976) Acta Cryst , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 57
    • 33744807436 scopus 로고    scopus 로고
    • Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures
    • Damm KL, Carlson HA, (2006) Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures. Biophys J 90: 4558-4573.
    • (2006) Biophys J , vol.90 , pp. 4558-4573
    • Damm, K.L.1    Carlson, H.A.2
  • 58
    • 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, (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
  • 59
    • 2442676589 scopus 로고    scopus 로고
    • Automated structure prediction of weakly homologous proteins on a genomic scale
    • Zhang Y, Skolnick J, (2004) Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci U S A 101: 7594-7599.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 7594-7599
    • Zhang, Y.1    Skolnick, J.2
  • 60
    • 0000243829 scopus 로고
    • PROCHECK: a program to check the stereochemical quality of protein structures
    • Laskowski RA, MacArthur MW, Moss DS, Thornton JM, (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26: 283-291.
    • (1993) J Appl Cryst , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 61
    • 0038820376 scopus 로고    scopus 로고
    • AstexViewer: a visualisation aid for structure-based drug design
    • Hartshorn MJ, (2002) AstexViewer: a visualisation aid for structure-based drug design. J Comput Aided Mol Des 16: 871-881.
    • (2002) J Comput Aided Mol Des , vol.16 , pp. 871-881
    • Hartshorn, M.J.1
  • 62
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: a simple approach to improve protein structure predictions
    • Ginalski K, Elofsson A, Fischer D, 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
  • 63
    • 0043123216 scopus 로고    scopus 로고
    • GeneSilico protein structure prediction meta-server
    • Kurowski MA, Bujnicki JM, (2003) GeneSilico protein structure prediction meta-server. Nucleic Acids Res 31: 3305-3307.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3305-3307
    • Kurowski, M.A.1    Bujnicki, J.M.2
  • 64
    • 34547612652 scopus 로고    scopus 로고
    • Pcons.net: protein structure prediction meta server
    • Wallner B, Larsson P, Elofsson A, (2007) Pcons.net: protein structure prediction meta server. Nucleic Acids Res 35: W369-374.
    • (2007) Nucleic Acids Res , vol.35
    • Wallner, B.1    Larsson, P.2    Elofsson, A.3
  • 65
    • 33745616114 scopus 로고    scopus 로고
    • A machine learning information retrieval approach to protein fold recognition
    • Cheng J, Baldi P, (2006) A machine learning information retrieval approach to protein fold recognition. Bioinformatics 22: 1456-1463.
    • (2006) Bioinformatics , vol.22 , pp. 1456-1463
    • Cheng, J.1    Baldi, P.2
  • 66
    • 13244289774 scopus 로고    scopus 로고
    • Descriptor-based protein remote homology identification
    • Zhang Z, Kochhar S, Grigorov MG, (2005) Descriptor-based protein remote homology identification. Protein Sci 14: 431-444.
    • (2005) Protein Sci , vol.14 , pp. 431-444
    • Zhang, Z.1    Kochhar, S.2    Grigorov, M.G.3
  • 67
    • 20744433230 scopus 로고    scopus 로고
    • Fold recognition by combining profile-profile alignment and support vector machine
    • Han S, Lee BC, Yu ST, Jeong CS, Lee S, et al. (2005) Fold recognition by combining profile-profile alignment and support vector machine. Bioinformatics 21: 2667-2673.
    • (2005) Bioinformatics , vol.21 , pp. 2667-2673
    • Han, S.1    Lee, B.C.2    Yu, S.T.3    Jeong, C.S.4    Lee, S.5
  • 68
    • 33646075470 scopus 로고    scopus 로고
    • Multiple mapping method: a novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling
    • Rai BK, Fiser A, (2006) Multiple mapping method: a novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling. Proteins 63: 644-661.
    • (2006) Proteins , vol.63 , pp. 644-661
    • Rai, B.K.1    Fiser, A.2
  • 69
    • 30344466041 scopus 로고    scopus 로고
    • FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6
    • Kosinski J, Gajda MJ, Cymerman IA, Kurowski MA, Pawlowski M, et al. (2005) FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6. Proteins 61Suppl 7: 106-113.
    • (2005) Proteins , vol.61 , pp. 106-113
    • Kosinski, J.1    Gajda, M.J.2    Cymerman, I.A.3    Kurowski, M.A.4    Pawlowski, M.5
  • 70
    • 67649535959 scopus 로고    scopus 로고
    • Improving consensus contact prediction via server correlation reduction
    • Gao X, Bu D, Xu J, Li M, (2009) Improving consensus contact prediction via server correlation reduction. BMC Struct Biol 9: 28.
    • (2009) BMC Struct Biol , vol.9 , pp. 28
    • Gao, X.1    Bu, D.2    Xu, J.3    Li, M.4
  • 71
    • 17144369578 scopus 로고    scopus 로고
    • Protein folding rates estimated from contact predictions
    • Punta M, Rost B, (2005) Protein folding rates estimated from contact predictions. J Mol Biol 348: 507-512.
    • (2005) J Mol Biol , vol.348 , pp. 507-512
    • Punta, M.1    Rost, B.2
  • 72
    • 77951961719 scopus 로고    scopus 로고
    • How significant is a protein structure similarity with TM-score = 0.5?
    • Xu J, Zhang Y, (2010) How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics 26: 889-895.
    • (2010) Bioinformatics , vol.26 , pp. 889-895
    • Xu, J.1    Zhang, Y.2
  • 73
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost B, (1999) Twilight zone of protein sequence alignments. Protein Eng 12: 85-94.
    • (1999) Protein Eng , vol.12 , pp. 85-94
    • Rost, B.1
  • 74
    • 34547620863 scopus 로고    scopus 로고
    • Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field
    • Kmiecik S, Gront D, Kolinski A, (2007) Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field. BMC Struct Biol 7: 43.
    • (2007) BMC Struct Biol , vol.7 , pp. 43
    • Kmiecik, S.1    Gront, D.2    Kolinski, A.3
  • 75
    • 0037079585 scopus 로고    scopus 로고
    • Identifying native-like protein structures using physics-based potentials
    • Dominy BN, Brooks CL, (2002) Identifying native-like protein structures using physics-based potentials. J Comput Chem 23: 147-160.
    • (2002) J Comput Chem , vol.23 , pp. 147-160
    • Dominy, B.N.1    Brooks, C.L.2
  • 76
    • 0035914481 scopus 로고    scopus 로고
    • Molecular dynamics in the endgame of protein structure prediction
    • Lee MR, Tsai J, Baker D, Kollman PA, (2001) Molecular dynamics in the endgame of protein structure prediction. J Mol Biol 313: 417-430.
    • (2001) J Mol Biol , vol.313 , pp. 417-430
    • Lee, M.R.1    Tsai, J.2    Baker, D.3    Kollman, P.A.4
  • 77
    • 0032512619 scopus 로고    scopus 로고
    • Rapid refinement of protein interfaces incorporating solvation: application to the docking problem
    • Jackson RM, Gabb HA, Sternberg MJ, (1998) Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J Mol Biol 276: 265-285.
    • (1998) J Mol Biol , vol.276 , pp. 265-285
    • Jackson, R.M.1    Gabb, H.A.2    Sternberg, M.J.3
  • 78
    • 76149120388 scopus 로고    scopus 로고
    • AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
    • Trott O, Olson AJ, (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31: 455-461.
    • (2010) J Comput Chem , vol.31 , pp. 455-461
    • Trott, O.1    Olson, A.J.2
  • 80
    • 77953052604 scopus 로고    scopus 로고
    • Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling
    • Brylinski M, Skolnick J, (2010) Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling. J Comput Chem 31: 1093-1105.
    • (2010) J Comput Chem , vol.31 , pp. 1093-1105
    • Brylinski, M.1    Skolnick, J.2


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