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Volumn 58, Issue 2, 2018, Pages 287-296

KDEEP: Protein-Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; COMPLEXATION; COMPUTATIONAL CHEMISTRY; CONVOLUTION; CORRELATION METHODS; FORECASTING; LIGANDS; MACHINE LEARNING; PROTEINS;

EID: 85042374412     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.7b00650     Document Type: Article
Times cited : (685)

References (61)
  • 1
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking J. Mol. Biol. 1997, 267, 727-748 10.1006/jmbi.1996.0897
    • (1997) J. Mol. Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 2
    • 0037434582 scopus 로고    scopus 로고
    • Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine
    • Jain, A. N. Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine J. Med. Chem. 2003, 46, 499-511 10.1021/jm020406h
    • (2003) J. Med. Chem. , vol.46 , pp. 499-511
    • Jain, A.N.1
  • 4
    • 76149120388 scopus 로고    scopus 로고
    • AutoDock Vina
    • Trott, O.; Olson, A. J. AutoDock Vina J. Comput. Chem. 2010, 31, 445-461 10.1002/jcc.21334
    • (2010) J. Comput. Chem. , vol.31 , pp. 445-461
    • Trott, O.1    Olson, A.J.2
  • 5
    • 77952415408 scopus 로고    scopus 로고
    • Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field
    • Shivakumar, D.; Williams, J.; Wu, Y.; Damm, W.; Shelley, J.; Sherman, W. Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field J. Chem. Theory Comput. 2010, 6, 1509-1519 10.1021/ct900587b
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 1509-1519
    • Shivakumar, D.1    Williams, J.2    Wu, Y.3    Damm, W.4    Shelley, J.5    Sherman, W.6
  • 7
    • 85018602823 scopus 로고    scopus 로고
    • Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation
    • Wan, S.; Bhati, A. P.; Skerratt, S.; Omoto, K.; Shanmugasundaram, V.; Bagal, S. K.; Coveney, P. V. Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation J. Chem. Inf. Model. 2017, 57, 897-909 10.1021/acs.jcim.6b00780
    • (2017) J. Chem. Inf. Model. , vol.57 , pp. 897-909
    • Wan, S.1    Bhati, A.P.2    Skerratt, S.3    Omoto, K.4    Shanmugasundaram, V.5    Bagal, S.K.6    Coveney, P.V.7
  • 10
    • 84945475267 scopus 로고    scopus 로고
    • Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening
    • Ain, Q. U.; Aleksandrova, A.; Roessler, F. D.; Ballester, P. J. Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2015, 5, 405-424 10.1002/wcms.1225
    • (2015) Wiley Interdiscip. Rev.: Comput. Mol. Sci. , vol.5 , pp. 405-424
    • Ain, Q.U.1    Aleksandrova, A.2    Roessler, F.D.3    Ballester, P.J.4
  • 11
    • 0037763817 scopus 로고    scopus 로고
    • Comparative evaluation of 11 scoring functions for molecular docking
    • Wang, R.; Lu, Y.; Wang, S. Comparative evaluation of 11 scoring functions for molecular docking J. Med. Chem. 2003, 46, 2287-2303 10.1021/jm0203783
    • (2003) J. Med. Chem. , vol.46 , pp. 2287-2303
    • Wang, R.1    Lu, Y.2    Wang, S.3
  • 12
    • 52249113723 scopus 로고    scopus 로고
    • SFCscore: Scoring functions for affinity prediction of protein-ligand complexes
    • Sotriffer, C. A.; Sanschagrin, P.; Matter, H.; Klebe, G. SFCscore: Scoring functions for affinity prediction of protein-ligand complexes Proteins: Struct., Funct., Genet. 2008, 73, 395-419 10.1002/prot.22058
    • (2008) Proteins: Struct., Funct., Genet. , vol.73 , pp. 395-419
    • Sotriffer, C.A.1    Sanschagrin, P.2    Matter, H.3    Klebe, G.4
  • 13
    • 77952825581 scopus 로고    scopus 로고
    • A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking
    • Ballester, P. J.; Mitchell, J. B. O. A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking Bioinformatics 2010, 26, 1169-1175 10.1093/bioinformatics/btq112
    • (2010) Bioinformatics , vol.26 , pp. 1169-1175
    • Ballester, P.J.1    Mitchell, J.B.O.2
  • 14
    • 0035478854 scopus 로고    scopus 로고
    • Random Forests
    • Breiman, L. Random Forests Mach. Learn. 2001, 45, 5-32 10.1023/A:1010933404324
    • (2001) Mach. Learn. , vol.45 , pp. 5-32
    • Breiman, L.1
  • 15
    • 84875428269 scopus 로고    scopus 로고
    • ID-score: A new empirical scoring function based on a comprehensive set of descriptors related to protein-ligand interactions
    • Li, G. B.; Yang, L. L.; Wang, W. J.; Li, L. L.; Yang, S. Y. ID-score: A new empirical scoring function based on a comprehensive set of descriptors related to protein-ligand interactions J. Chem. Inf. Model. 2013, 53, 592-600 10.1021/ci300493w
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 592-600
    • Li, G.B.1    Yang, L.L.2    Wang, W.J.3    Li, L.L.4    Yang, S.Y.5
  • 16
    • 34249753618 scopus 로고
    • Support vector machine
    • Cortes, C.; Vapnik, V. Support vector machine Mach. Learn. 1995, 20, 273-297 10.1007/BF00994018
    • (1995) Mach. Learn. , vol.20 , pp. 273-297
    • Cortes, C.1    Vapnik, V.2
  • 17
    • 84923588607 scopus 로고    scopus 로고
    • Improving autodock vina using random forest: The growing accuracy of binding affinity prediction by the effective exploitation of larger data sets
    • Li, H.; Leung, K. S.; Wong, M. H.; Ballester, P. J. Improving autodock vina using random forest: The growing accuracy of binding affinity prediction by the effective exploitation of larger data sets Mol. Inf. 2015, 34, 115-126 10.1002/minf.201400132
    • (2015) Mol. Inf. , vol.34 , pp. 115-126
    • Li, H.1    Leung, K.S.2    Wong, M.H.3    Ballester, P.J.4
  • 18
    • 84883250593 scopus 로고    scopus 로고
    • SFCscoreRF: A Random Forest-Based Scoring Function for Improved Affinity Prediction of Protein-Ligand Complexes
    • Zilian, D.; Sotri, C. SFCscoreRF: A Random Forest-Based Scoring Function for Improved Affinity Prediction of Protein-Ligand Complexes J. Chem. Inf. Model. 2013, 53, 1923-1933 10.1021/ci400120b
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 1923-1933
    • Zilian, D.1    Sotri, C.2
  • 19
    • 84930630277 scopus 로고    scopus 로고
    • Deep learning
    • LeCun, Y.; Bengio, Y.; Hinton, G. Deep learning Nature 2015, 521, 436-444 10.1038/nature14539
    • (2015) Nature , vol.521 , pp. 436-444
    • LeCun, Y.1    Bengio, Y.2    Hinton, G.3
  • 20
    • 84910651844 scopus 로고    scopus 로고
    • Deep Learning in Neural Networks: An Overview
    • Schmidhuber, J. Deep Learning in Neural Networks: An Overview Neural Netw. 2015, 61, 85-117 10.1016/j.neunet.2014.09.003
    • (2015) Neural Netw. , vol.61 , pp. 85-117
    • Schmidhuber, J.1
  • 22
    • 85001976188 scopus 로고    scopus 로고
    • A primer on neural network models for natural language processing
    • Goldberg, Y. A primer on neural network models for natural language processing J. Artif. Intell. Res. 2016, 57, 345-420
    • (2016) J. Artif. Intell. Res. , vol.57 , pp. 345-420
    • Goldberg, Y.1
  • 25
    • 85030705791 scopus 로고    scopus 로고
    • DeepSite: Protein-binding site predictor using 3D-convolutional neural networks
    • Jiménez, J.; Doerr, S.; Martínez-Rosell, G.; Rose, A. S.; De Fabritiis, G. DeepSite: protein-binding site predictor using 3D-convolutional neural networks Bioinformatics 2017, 33, 3036-3042 10.1093/bioinformatics/btx350
    • (2017) Bioinformatics , vol.33 , pp. 3036-3042
    • Jiménez, J.1    Doerr, S.2    Martínez-Rosell, G.3    Rose, A.S.4    De Fabritiis, G.5
  • 27
  • 28
    • 85026627894 scopus 로고    scopus 로고
    • TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions
    • Cang, Z.; Wei, G. TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions PLoS Comput. Biol. 2017, 13, e1005690 10.1371/journal.pcbi.1005690
    • (2017) PLoS Comput. Biol. , vol.13 , pp. e1005690
    • Cang, Z.1    Wei, G.2
  • 29
    • 85008475964 scopus 로고    scopus 로고
    • Boosting Docking-Based Virtual Screening with Deep Learning
    • Pereira, J. C.; Caffarena, E. R.; Dos Santos, C. N. Boosting Docking-Based Virtual Screening with Deep Learning J. Chem. Inf. Model. 2016, 56, 2495-2506 10.1021/acs.jcim.6b00355
    • (2016) J. Chem. Inf. Model. , vol.56 , pp. 2495-2506
    • Pereira, J.C.1    Caffarena, E.R.2    Dos Santos, C.N.3
  • 30
    • 85027440798 scopus 로고    scopus 로고
    • Performance of machine-learning scoring functions in structure-based virtual screening
    • Wójcikowski, M.; Ballester, P. J.; Siedlecki, P. Performance of machine-learning scoring functions in structure-based virtual screening Sci. Rep. 2017, 7, 46710 10.1038/srep46710
    • (2017) Sci. Rep. , vol.7 , pp. 46710
    • Wójcikowski, M.1    Ballester, P.J.2    Siedlecki, P.3
  • 31
    • 84880542260 scopus 로고    scopus 로고
    • Deep architectures and deep learning in chemoinformatics: The prediction of aqueous solubility for drug-like molecules
    • Lusci, A.; Pollastri, G.; Baldi, P. Deep architectures and deep learning in chemoinformatics: The prediction of aqueous solubility for drug-like molecules J. Chem. Inf. Model. 2013, 53, 1563-1575 10.1021/ci400187y
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 1563-1575
    • Lusci, A.1    Pollastri, G.2    Baldi, P.3
  • 33
    • 85026913013 scopus 로고    scopus 로고
    • The inner and outer approaches to the design of recursive neural architectures
    • Baldi, P. The inner and outer approaches to the design of recursive neural architectures Data Min. Knowl. Discov 2018, 32, 218 10.1007/s10618-017-0531-0
    • (2018) Data Min. Knowl. Discov , vol.32 , pp. 218
    • Baldi, P.1
  • 34
    • 85013653033 scopus 로고    scopus 로고
    • Forging the Basis for Developing Protein-Ligand Interaction Scoring Functions
    • Liu, Z.; Su, M.; Han, L.; Liu, J.; Yang, Q.; Li, Y.; Wang, R. Forging the Basis for Developing Protein-Ligand Interaction Scoring Functions Acc. Chem. Res. 2017, 50, 302-309 10.1021/acs.accounts.6b00491
    • (2017) Acc. Chem. Res. , vol.50 , pp. 302-309
    • Liu, Z.1    Su, M.2    Han, L.3    Liu, J.4    Yang, Q.5    Li, Y.6    Wang, R.7
  • 35
    • 85008692166 scopus 로고    scopus 로고
    • CSM-lig: A web server for assessing and comparing protein-small molecule affinities
    • Pires, D. E.; Ascher, D. B. CSM-lig: a web server for assessing and comparing protein-small molecule affinities Nucleic Acids Res. 2016, 44, W557-W561 10.1093/nar/gkw390
    • (2016) Nucleic Acids Res. , vol.44 , pp. W557-W561
    • Pires, D.E.1    Ascher, D.B.2
  • 36
    • 84894639153 scopus 로고    scopus 로고
    • Istar: A web platform for large-scale protein-ligand docking
    • Li, H.; Leung, K. S.; Ballester, P. J.; Wong, M. H. Istar: A web platform for large-scale protein-ligand docking. PLoS One 2014, 9. e85678 10.1371/journal.pone.0085678
    • (2014) PLoS One , vol.9 , pp. e85678
    • Li, H.1    Leung, K.S.2    Ballester, P.J.3    Wong, M.H.4
  • 37
    • 84903302003 scopus 로고    scopus 로고
    • Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set
    • Li, Y.; Liu, Z.; Li, J.; Han, L.; Liu, J.; Zhao, Z.; Wang, R. Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set J. Chem. Inf. Model. 2014, 54, 1700-1716 10.1021/ci500080q
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 1700-1716
    • Li, Y.1    Liu, Z.2    Li, J.3    Han, L.4    Liu, J.5    Zhao, Z.6    Wang, R.7
  • 38
    • 66149103553 scopus 로고    scopus 로고
    • Comparative Assessment of Scoring Functions on a Diverse Test Set
    • Cheng, T.; Li, X.; Li, Y.; Liu, Z.; Wang, R. Comparative Assessment of Scoring Functions on a Diverse Test Set J. Chem. Inf. Model. 2009, 49, 1079-1093 10.1021/ci9000053
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1079-1093
    • Cheng, T.1    Li, X.2    Li, Y.3    Liu, Z.4    Wang, R.5
  • 39
    • 84908242076 scopus 로고    scopus 로고
    • Beware of machine learning-based scoring functions-on the danger of developing black boxes
    • Gabel, J.; Desaphy, J.; Rognan, D. Beware of machine learning-based scoring functions-on the danger of developing black boxes J. Chem. Inf. Model. 2014, 54, 2807-2815 10.1021/ci500406k
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 2807-2815
    • Gabel, J.1    Desaphy, J.2    Rognan, D.3
  • 40
    • 78649517318 scopus 로고    scopus 로고
    • Leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets
    • Kramer, C.; Gedeck, P. Leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets J. Chem. Inf. Model. 2010, 50, 1961-1969 10.1021/ci100264e
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 1961-1969
    • Kramer, C.1    Gedeck, P.2
  • 41
    • 80051984855 scopus 로고    scopus 로고
    • Comments on "leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets": Significance for the validation of scoring functions
    • Ballester, P. J.; Mitchell, J. B. O. Comments on "leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets": Significance for the validation of scoring functions J. Chem. Inf. Model. 2011, 51, 1739-1741 10.1021/ci200057e
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 1739-1741
    • Ballester, P.J.1    Mitchell, J.B.O.2
  • 45
    • 85042722566 scopus 로고    scopus 로고
    • RDKit: Open-source cheminformatics, (accessed January 2018)
    • Landrum, G. RDKit: Open-source cheminformatics, 2012. http://www.rdkit.org (accessed January 2018).
    • (2012)
    • Landrum, G.1
  • 47
    • 84964649164 scopus 로고    scopus 로고
    • HTMD: High-Throughput Molecular Dynamics for Molecular Discovery
    • Doerr, S.; Harvey, M. J.; Noé, F.; De Fabritiis, G. HTMD: High-Throughput Molecular Dynamics for Molecular Discovery J. Chem. Theory Comput. 2016, 12, 1845-1852 10.1021/acs.jctc.6b00049
    • (2016) J. Chem. Theory Comput. , vol.12 , pp. 1845-1852
    • Doerr, S.1    Harvey, M.J.2    Noé, F.3    De Fabritiis, G.4
  • 48
    • 84986274465 scopus 로고    scopus 로고
    • Deep Residual Learning for Image Recognition; IEEE CVPR
    • He, K.; Zhang, X.; Ren, S.; Sun, J. Deep Residual Learning for Image Recognition; IEEE CVPR; 2016; pp 770-778.
    • (2016) , pp. 770-778
    • He, K.1    Zhang, X.2    Ren, S.3    Sun, J.4
  • 49
    • 85083953063 scopus 로고    scopus 로고
    • Very Deep Convolutional Networks for Large-Scale Image Recognition
    • Simonyan, K.; Zisserman, A. Very Deep Convolutional Networks for Large-Scale Image Recognition Int. Conf. Learn. Represent. 2015, 1-14
    • (2015) Int. Conf. Learn. Represent. , pp. 1-14
    • Simonyan, K.1    Zisserman, A.2
  • 53
    • 84862277874 scopus 로고    scopus 로고
    • Understanding the difficulty of training deep feedforward neural networks
    • Glorot, X.; Bengio, Y. Understanding the difficulty of training deep feedforward neural networks AISTATS 13 2010, 9, 249-256
    • (2010) AISTATS 13 , vol.9 , pp. 249-256
    • Glorot, X.1    Bengio, Y.2
  • 54
    • 0036022960 scopus 로고    scopus 로고
    • Further development and validation of empirical scoring functions for structure-based binding affinity prediction
    • Wang, R.; Lai, L.; Wang, S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction J. Comput.-Aided Mol. Des. 2002, 16, 11-26 10.1023/A:1016357811882
    • (2002) J. Comput.-Aided Mol. Des. , vol.16 , pp. 11-26
    • Wang, R.1    Lai, L.2    Wang, S.3
  • 55
    • 84902438255 scopus 로고    scopus 로고
    • Improved protein-ligand binding affinity prediction by using a curvature-dependent surface-area model
    • Cao, Y.; Li, L. Improved protein-ligand binding affinity prediction by using a curvature-dependent surface-area model Bioinformatics 2014, 30, 1674-1680 10.1093/bioinformatics/btu104
    • (2014) Bioinformatics , vol.30 , pp. 1674-1680
    • Cao, Y.1    Li, L.2
  • 57
    • 77649229098 scopus 로고    scopus 로고
    • Binding affinity prediction with property-encoded shape distribution signatures
    • Das, S.; Krein, M. P.; Breneman, C. M. Binding affinity prediction with property-encoded shape distribution signatures J. Chem. Inf. Model. 2010, 50, 298-308 10.1021/ci9004139
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 298-308
    • Das, S.1    Krein, M.P.2    Breneman, C.M.3
  • 58
    • 84938280812 scopus 로고    scopus 로고
    • Low-quality structural and interaction data improves binding affinity prediction via random forest
    • Li, H.; Leung, K. S.; Wong, M. H.; Ballester, P. J. Low-quality structural and interaction data improves binding affinity prediction via random forest Molecules 2015, 20, 10947-10962 10.3390/molecules200610947
    • (2015) Molecules , vol.20 , pp. 10947-10962
    • Li, H.1    Leung, K.S.2    Wong, M.H.3    Ballester, P.J.4
  • 59
    • 85025625893 scopus 로고    scopus 로고
    • PlayMolecule ProteinPrepare: A Web Application for Protein Preparation for Molecular Dynamics Simulations
    • Martínez-Rosell, G.; Giorgino, T.; De Fabritiis, G. PlayMolecule ProteinPrepare: A Web Application for Protein Preparation for Molecular Dynamics Simulations J. Chem. Inf. Model. 2017, 57, 1511-1516 10.1021/acs.jcim.7b00190
    • (2017) J. Chem. Inf. Model. , vol.57 , pp. 1511-1516
    • Martínez-Rosell, G.1    Giorgino, T.2    De Fabritiis, G.3
  • 60
    • 85042708432 scopus 로고    scopus 로고
    • Theano Development Team. Theano: A Python framework for fast computation ofmathematicalexpressions, (, arXiv:1605.02688
    • Theano Development Team. Theano: A Python framework for fast computation ofmathematicalexpressions, (2016, arXiv:1605.02688.
    • (2016)
  • 61
    • 84995688316 scopus 로고    scopus 로고
    • Correcting the impact of docking pose generation error on binding affinity prediction
    • Li, H.; Leung, K.-S.; Wong, M.-H.; Ballester, P. J. Correcting the impact of docking pose generation error on binding affinity prediction BMC Bioinf. 2016, 17, 308 10.1186/s12859-016-1169-4
    • (2016) BMC Bioinf. , vol.17 , pp. 308
    • Li, H.1    Leung, K.-S.2    Wong, M.-H.3    Ballester, P.J.4


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