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Volumn 40, Issue 4, 2011, Pages 417-425

A machine learning-based method for protein global model quality assessment

Author keywords

model quality assessment; protein structure prediction; support vector regression

Indexed keywords

3D COORDINATES; CROSS VALIDATION; DATA SETS; EXISTING METHOD; GLOBAL MODELS; GOOD CORRELATIONS; INPUT AND OUTPUTS; MACHINE-LEARNING; MODEL QUALITIES; NATIVE STRUCTURES; PROTEIN MODELS; PROTEIN STRUCTURE PREDICTION; SECONDARY STRUCTURES; SOLVENT ACCESSIBILITY; STRUCTURAL FEATURE; SUPPORT VECTOR REGRESSION; SUPPORT VECTOR REGRESSIONS; WEB SERVERS;

EID: 79952673719     PISSN: 03081079     EISSN: 15635104     Source Type: Journal    
DOI: 10.1080/03081079.2010.544869     Document Type: Article
Times cited : (5)

References (33)
  • 1
    • 40549141792 scopus 로고    scopus 로고
    • QMEAN: A comprehensive scoring function for model quality assessment
    • DOI 10.1002/prot.21715
    • Benkert, P., Tosatto, S.C. and Schomburg, D., 2008. QMEAN: A comprehensive scoring function for model quality assessment. Proteins, 71 (1), 261-277, Journal Article Research Support, Non-US Gov't. (Pubitemid 351358609)
    • (2008) Proteins: Structure, Function and Genetics , vol.71 , Issue.1 , pp. 261-277
    • Benkert, P.1    Tosatto, S.C.E.2    Schomburg, D.3
  • 2
    • 0035103763 scopus 로고    scopus 로고
    • LiveBench-1: Continuous benchmarking of protein structure prediction servers
    • DOI 10.1110/ps.40501
    • Bujnicki, J.M., Elofsson, A., Fischer, D. and Rychlewski, L., 2001. LiveBench-1: Continuous benchmarking of protein structure prediction servers. Protein science, 10 (2), 352-361, Comparative Study Journal Article. (Pubitemid 32225655)
    • (2001) Protein Science , vol.10 , Issue.2 , pp. 352-361
    • Bujnicki, J.M.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4
  • 4
    • 33947203766 scopus 로고    scopus 로고
    • Evaluation of the structural quality of modeled proteins by using globularity criteria
    • Journal Article Research Support, Non-US Gov't
    • Costantini, S., Facchiano, A.M. and Colonna, G., 2007. Evaluation of the structural quality of modeled proteins by using globularity criteria. BMC structural biology, 7, 9, Journal Article Research Support, Non-US Gov't.
    • (2007) BMC Structural Biology , vol.7 , Issue.9
    • Costantini, S.1    Facchiano, A.M.2    Colonna, G.3
  • 5
    • 36749043625 scopus 로고    scopus 로고
    • Assessment of predictions in the model quality assessment category
    • DOI 10.1002/prot.21669
    • Cozzetto, D., Kryshtafovych, A., Ceriani, M. and Tramontano, A., 2007. Assessment of predictions in the model quality assessment category. Proteins, 69 (Suppl 8), 175-183, Comparative Study Evaluation Studies Journal Article Research Support, N.I.H., Extramural Research Support, Non-US Gov't. (Pubitemid 350210125)
    • (2007) Proteins: Structure, Function and Genetics , vol.69 , Issue.SUPPL. 8 , pp. 175-183
    • Cozzetto, D.1    Kryshtafovych, A.2    Ceriani, M.3    Tramontano, A.4
  • 6
    • 44949128253 scopus 로고    scopus 로고
    • Achieving 80 secondary structure prediction by large-scale training
    • Dor, O. and Zhou, Y., 2006. Achieving 80 secondary structure prediction by large-scale training. Proteins, 66 (4), 838-845.
    • (2006) Proteins , vol.66 , Issue.4 , pp. 838-845
    • Dor, O.1    Zhou, Y.2
  • 7
    • 34547576789 scopus 로고    scopus 로고
    • Local quality assessment in homology models using statistical potentials and support vector machines
    • DOI 10.1110/ps.072856307
    • Fasnacht, M., Zhu, J. and Honig, B., 2007. Local quality assessment in homology models using statistical potentials and support vector machines. Protein science, 16 (8), 1557-1568, Journal Article Research Support, N.I.H., Extramural Research Support, Non-US Gov't. (Pubitemid 47195683)
    • (2007) Protein Science , vol.16 , Issue.8 , pp. 1557-1568
    • Fasnacht, M.1    Zhu, J.2    Honig, B.3
  • 8
    • 34748842218 scopus 로고    scopus 로고
    • β statistical potentials can outperform all-atom potentials in decoy identification
    • DOI 10.1110/ps.072939707
    • Fitzgerald, J.E., et al., 2007. Reduced C(beta) statistical potentials can outperform all-atom potentials in decoy identification. Protein science, 16 (10), 2123-2139, Evaluation Studies Journal Article. (Pubitemid 47481648)
    • (2007) Protein Science , vol.16 , Issue.10 , pp. 2123-2139
    • Fitzgerald, J.E.1    Jha, A.K.2    Colubri, A.3    Sosnick, T.R.4    Freed, K.F.5
  • 9
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: A simple approach to improve protein structure predictions
    • DOI 10.1093/bioinformatics/btg124
    • Ginalski, K., Elofsson, A., Fischer, D. and Rychlewski, L., 2003. 3D-Jury: A simple approach to improve protein structure predictions. Bioinformatics, 19 (8), 1015-1018, 1367-4803, Evaluation Studies Journal Article Validation Studies. (Pubitemid 36675823)
    • (2003) Bioinformatics , vol.19 , Issue.8 , pp. 1015-1018
    • Ginalski, K.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4
  • 10
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculation with the new program DYANA
    • DOI 10.1006/jmbi.1997.1284
    • Guntert, P., Mumenthaler, C. and Wuthrich, K., 1997. Torsion angle dynamics for NMR structure calculation with the new program DYANA. Journal of molecular biology, 273 (1), 283-298. (Pubitemid 27460230)
    • (1997) Journal of Molecular Biology , vol.273 , Issue.1 , pp. 283-298
    • Guntert, P.1    Mumenthaler, C.2    Wuthrich, K.3
  • 11
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • DOI 10.1006/jmbi.1999.3091
    • Jones, D., 1999. Protein secondary structure based on position-specific scoring matrices. Journal of molecular biology, 292 (2), 195-202. (Pubitemid 29435759)
    • (1999) Journal of Molecular Biology , vol.292 , Issue.2 , pp. 195-202
    • Jones, D.T.1
  • 12
    • 0020997912 scopus 로고
    • Dictionary of secondary structure in proteins: Pattern recognition of hydrogenbonded and geometrical features
    • Kabsch, W. and Sander, C., 1983. Dictionary of secondary structure in proteins: Pattern recognition of hydrogenbonded and geometrical features. Biopolymers, 22 (12), 2577-2637.
    • (1983) Biopolymers , vol.22 , Issue.12 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 13
    • 0346458791 scopus 로고    scopus 로고
    • A new pairwise folding potential based on improved decoy generation and side-chain packing
    • DOI 10.1002/prot.10521
    • Loose, C., Klepeis, J.L. and Floudas, C.A., 2004. A new pairwise folding potential based on improved decoy generation and side-chain packing. Proteins, 54 (2), 303-314, Journal Article Research Support, US Gov't, Non-P.H.S. Research Support, US Gov't, P.H.S. (Pubitemid 38084071)
    • (2004) Proteins: Structure, Function and Genetics , vol.54 , Issue.2 , pp. 303-314
    • Loose, C.1    Klepeis, J.L.2    Floudas, C.A.3
  • 14
    • 38049051121 scopus 로고    scopus 로고
    • OPUS-PSP: An orientation-dependent statistical all-atom potential derived from side-chain packing
    • Journal Article Research Support, N.I.H., Extramural Research Support, Non-US Gov't Research Support, US Gov't, Non-P.H.S
    • Lu, M., Dousis, A.D. and Ma, J., 2008. OPUS-PSP: An orientation-dependent statistical all-atom potential derived from side-chain packing. Journal of molecular biology, 376 (1), 288-301, Journal Article Research Support, N.I.H., Extramural Research Support, Non-US Gov't Research Support, US Gov't, Non-P.H.S.
    • (2008) Journal of molecular biology , vol.376 , Issue.1 , pp. 288-301
    • Lu, M.1    Dousis, A.D.2    Ma, J.3
  • 15
    • 41549086671 scopus 로고    scopus 로고
    • Validation of protein models by a neural network approach
    • Evaluation Studies Journal Article Validation Studies
    • Mereghetti, P., et al., 2008. Validation of protein models by a neural network approach. BMC bioinformatics, 9, 66, Evaluation Studies Journal Article Validation Studies.
    • (2008) BMC bioinformatics , vol.9 , Issue.66
    • Mereghetti, P.1
  • 16
    • 38349161685 scopus 로고    scopus 로고
    • An information theoretic approach for improving data driven prediction of protein model quality
    • Montuori, A., Raimondo, G. and Pasero, E., 2008. An information theoretic approach for improving data driven prediction of protein model quality. Computers and mathematics with applications, 55 (5), 997-1006.
    • (2008) Computers and mathematics with applications , vol.55 , Issue.5 , pp. 997-1006
    • Montuori, A.1    Raimondo, G.2    Pasero, E.3
  • 18
    • 24344479166 scopus 로고    scopus 로고
    • Atomically detailed potentials to recognize native and approximate protein structures
    • DOI 10.1002/prot.20585
    • Qiu, J. and Elber, R., 2005. Atomically detailed potentials to recognize native and approximate protein structures. Proteins, 61 (1), 44-55, Journal Article. (Pubitemid 41262916)
    • (2005) Proteins: Structure, Function and Genetics , vol.61 , Issue.1 , pp. 44-55
    • Qiu, J.1    Elber, R.2
  • 19
    • 38549146473 scopus 로고    scopus 로고
    • Distance dependent centroid to centroid force fields using high resolution decoys
    • DOI 10.1002/prot.21561
    • Rajgaria, R., McAllister, S.R. and Floudas, C.A., 2008. Distance dependent centroid to centroid force fields using high resolution decoys. Proteins, 70 (3), 950-970, Journal Article Research Support, N.I.H., Extramural Research Support, US Gov't, Non-P.H.S. (Pubitemid 351161953)
    • (2008) Proteins: Structure, Function and Genetics , vol.70 , Issue.3 , pp. 950-970
    • Rajgaria, R.1    McAllister, S.R.2    Floudas, C.A.3
  • 20
    • 0033670439 scopus 로고    scopus 로고
    • MaxSub: An automated measure for the assessment of protein structure prediction quality
    • Evaluation Studies Journal Article Research Support, Non-US Gov't
    • Siew, N., Eloffson, A., Rychlewski, L. and Fischer, D., 2000. MaxSub: An automated measure for the assessment of protein structure prediction quality. Bioinformatics, 16 (9), 776-785, Evaluation Studies Journal Article Research Support, Non-US Gov't.
    • (2000) Bioinformatics , vol.16 , Issue.9 , pp. 776-785
    • Siew, N.1    Eloffson, A.2    Rychlewski, L.3    Fischer, D.4
  • 21
    • 33847673583 scopus 로고    scopus 로고
    • Near-native structure refinement using in vacuo energy minimization
    • DOI 10.1073/pnas.0611593104
    • Summa, C.M. and Levitt, M., 2007. Near-native structure refinement using in vacuo energy minimization. Proceedings of the national academy of sciences of the United States of America, 104 (9), 3177-3182, Journal Article Research Support, N.I.H., Extramural Research Support, US Gov't, Non-P.H.S. (Pubitemid 46364133)
    • (2007) Proceedings of the National Academy of Sciences of the United States of America , vol.104 , Issue.9 , pp. 3177-3182
    • Summa, C.M.1    Levitt, M.2
  • 22
    • 40949098547 scopus 로고    scopus 로고
    • Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction
    • Journal Article Research Support, Non-US Gov't
    • Tan, C.W. and Jones, D.T., 2008. Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction. BMC bioinformatics, 9, 94, Journal Article Research Support, Non-US Gov't.
    • (2008) BMC bioinformatics , vol.9 , pp. 94
    • Tan, C.W.1    Jones, D.T.2
  • 23
    • 28144448406 scopus 로고    scopus 로고
    • The Victor/FRST function for model quality estimation
    • DOI 10.1089/cmb.2005.12.1316
    • Tosatto, S.C., 2005. The Victor/FRST function for model quality estimation. Journal of computational biology, 12 (10), 1316-1327, Comparative Study Journal Article Research Support, Non-US Gov't. (Pubitemid 44743646)
    • (2005) Journal of Computational Biology , vol.12 , Issue.10 , pp. 1316-1327
    • Tosatto, S.C.E.1
  • 24
    • 34249778085 scopus 로고    scopus 로고
    • TAP score: Torsion angle propensity normalization applied to local protein structure evaluation
    • Comparative Study Journal Article Research Support, Non-US Gov't
    • Tosatto, S.C. and Battistutta, R., 2007. TAP score: Torsion angle propensity normalization applied to local protein structure evaluation. BMC bioinformatics, 8, 155, Comparative Study Journal Article Research Support, Non-US Gov't.
    • (2007) BMC bioinformatics , vol.8 , pp. 155
    • Tosatto, S.C.1    Battistutta, R.2
  • 26
    • 33947579390 scopus 로고    scopus 로고
    • Protein structure prediction by all-atom free-energy refinement
    • Verma, A. and Wenzel, W., 2007. Protein structure prediction by all-atom free-energy refinement. BMC structural biology, 7, 12.
    • (2007) BMC structural biology , vol.7 , pp. 12
    • Verma, A.1    Wenzel, W.2
  • 27
    • 0037406141 scopus 로고    scopus 로고
    • Can correct protein models be identified?
    • DOI 10.1110/ps.0236803
    • Wallner, B. and Elofsson, A., 2003. Can correct protein models be identified? Protein science, 12 (5), 1073-1086, Journal Article. (Pubitemid 36505441)
    • (2003) Protein Science , vol.12 , Issue.5 , pp. 1073-1086
    • Wallner, B.1    Elofsson, A.2
  • 28
    • 36749049687 scopus 로고    scopus 로고
    • Prediction of global and local model quality in CASP7 using Pcons and ProQ
    • DOI 10.1002/prot.21774
    • Wallner, B. and Elofsson, A., 2007. Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins, 69 (Suppl 8), 184-193. (Pubitemid 350210126)
    • (2007) Proteins: Structure, Function and Genetics , vol.69 , Issue.SUPPL. 8 , pp. 184-193
    • Wallner, B.1    Elofsson, A.2
  • 29
    • 66149156968 scopus 로고    scopus 로고
    • Evaluating the absolute quality of a single protein model using structural features and support vector machines
    • Wang, Z., Tegge, A.N. and Cheng, J., 2008. Evaluating the absolute quality of a single protein model using structural features and support vector machines. Proteins, 75, 638-647.
    • (2008) Proteins , vol.75 , pp. 638-647
    • Wang, Z.1    Tegge, A.N.2    Cheng, J.3
  • 30
    • 39449115394 scopus 로고    scopus 로고
    • I-TASSER server for protein 3D structure prediction
    • Journal Article Research Support, Non-US Gov't
    • Zhang, Y., 2008. I-TASSER server for protein 3D structure prediction. BMC bioinformatics, 9, 40, Journal Article Research Support, Non-US Gov't.
    • (2008) BMC bioinformatics , vol.9 , pp. 40
    • Zhang, Y.1
  • 31
    • 1942519275 scopus 로고    scopus 로고
    • SPICKER: A clustering approach to identify near-native protein folds
    • Zhang, Y. and Skolnick, J., 2004. SPICKER: A clustering approach to identify near-native protein folds. Journal of computational chemistry, 25 (6), 865-871.
    • (2004) Journal of computational chemistry , vol.25 , Issue.6 , pp. 865-871
    • Zhang, Y.1    Skolnick, J.2
  • 32
    • 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
    • DOI 10.1110/ps.03348304
    • Zhang, C., Liu, S., Zhou, H. and 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 science, 13 (2), 400-411, Journal Article Research Support, Non-US Gov't Research Support, US Gov't, P.H.S. (Pubitemid 38124961)
    • (2004) Protein Science , vol.13 , Issue.2 , pp. 400-411
    • Zhang, C.1    Liu, S.2    Zhou, H.3    Zhou, Y.4
  • 33
    • 42449119311 scopus 로고    scopus 로고
    • α contact potential
    • DOI 10.1002/prot.21813
    • Zhou, H. and Skolnick, J., 2008. Protein model quality assessment prediction by combining fragment comparisons and a consensus C(alpha) contact potential. Proteins, 71 (3), 1211-1218, Article Research Support, N.I.H., Extramural. (Pubitemid 351564047)
    • (2008) Proteins: Structure, Function and Genetics , vol.71 , Issue.3 , pp. 1211-1218
    • Zhou, H.1    Skolnick, J.2


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