메뉴 건너뛰기




Volumn 8, Issue 1, 2018, Pages

The impact of protein structure and sequence similarity on the accuracy of machine-learning scoring functions for binding affinity prediction

Author keywords

Binding affinity prediction; Machine learning; Molecular docking; Scoring function

Indexed keywords

ARTICLE; BINDING AFFINITY; LINEAR REGRESSION ANALYSIS; MACHINE LEARNING; MOLECULAR DOCKING; PREDICTION; PROTEIN STRUCTURE; RANDOM FOREST; PROCEDURES; PROTEIN ANALYSIS; SEQUENCE ANALYSIS; STANDARDS;

EID: 85044292801     PISSN: None     EISSN: 2218273X     Source Type: Journal    
DOI: 10.3390/biom8010012     Document Type: Article
Times cited : (56)

References (26)
  • 1
    • 77952825581 scopus 로고    scopus 로고
    • A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking
    • [CrossRef][PubMed]
    • 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.[CrossRef][PubMed]
    • (2010) Bioinformatics , vol.26 , pp. 1169-1175
    • Ballester, P.J.1    Mitchell, J.B.O.2
  • 2
    • 84927634713 scopus 로고    scopus 로고
    • A comparative assessment of predictive accuracies of conventional and machine learning scoring functions for protein–ligand binding affinity prediction
    • [CrossRef][PubMed]
    • Ashtawy, H.M.; Mahapatra, N.R. A comparative assessment of predictive accuracies of conventional and machine learning scoring functions for protein–ligand binding affinity prediction. IEEE/ACM Trans. Comput. Biol. Bioinform. 2015, 12, 335–347.[CrossRef][PubMed]
    • (2015) IEEE/ACM Trans. Comput. Biol. Bioinform , vol.12 , pp. 335-347
    • Ashtawy, H.M.1    Mahapatra, N.R.2
  • 3
    • 84883250593 scopus 로고    scopus 로고
    • SFCscore(RF): A random forest-based scoring function for improved affinity prediction of protein–ligand complexes
    • [CrossRef][PubMed]
    • Zilian, D.; Sotriffer, C.A. SFCscore(RF): A random forest-based scoring function for improved affinity prediction of protein–ligand complexes. J. Chem. Inf. Model. 2013, 53, 1923–1933.[CrossRef][PubMed]
    • (2013) J. Chem. Inf. Model , vol.53 , pp. 1923-1933
    • Zilian, D.1    Sotriffer, C.A.2
  • 4
    • 80053313926 scopus 로고    scopus 로고
    • Support vector regression scoring of receptor–ligand complexes for rank-ordering and virtual screening of chemical libraries
    • [CrossRef][PubMed]
    • Li, L.; Wang, B.; Meroueh, S.O. Support vector regression scoring of receptor–ligand complexes for rank-ordering and virtual screening of chemical libraries. J. Chem. Inf. Model. 2011, 51, 2132–2138.[CrossRef][PubMed]
    • (2011) J. Chem. Inf. Model , vol.51 , pp. 2132-2138
    • Li, L.1    Wang, B.2    Meroueh, S.O.3
  • 5
    • 84873041650 scopus 로고    scopus 로고
    • Characterization of small molecule binding. I. Accurate identification of strong inhibitors in virtual screening
    • [PubMed]
    • Ding, B.; Wang, J.; Li, N.; Wang, W. Characterization of small molecule binding. I. Accurate identification of strong inhibitors in virtual screening. J. Chem. Inf. Model. 2013, 53, 114–122.[PubMed]
    • (2013) J. Chem. Inf. Model , vol.53 , pp. 114-122
    • Ding, B.1    Wang, J.2    Li, N.3    Wang, W.4
  • 6
    • 84995688316 scopus 로고    scopus 로고
    • Correcting the impact of docking pose generation error on binding affinity prediction
    • [CrossRef][PubMed]
    • Li, H.; Leung, K.; Wong, M.; Ballester, P.J. Correcting the impact of docking pose generation error on binding affinity prediction. BMC Bioinform. 2016, 17, 308.[CrossRef][PubMed]
    • (2016) BMC Bioinform , vol.17 , pp. 308
    • Li, H.1    Leung, K.2    Wong, M.3    Ballester, P.J.4
  • 7
    • 84964225053 scopus 로고    scopus 로고
    • Constructing and validating high-performance MIEC-SVM models in virtual screening for kinases: A better way for actives discovery
    • [CrossRef][PubMed]
    • Sun, H.; Pan, P.; Tian, S.; Xu, L.; Kong, X.; Li, Y.; Dan, L.; Hou, T. Constructing and validating high-performance MIEC-SVM models in virtual screening for kinases: A better way for actives discovery. Sci. Rep. 2016, 6, 24817.[CrossRef][PubMed]
    • (2016) Sci. Rep , vol.6 , pp. 24817
    • Sun, H.1    Pan, P.2    Tian, S.3    Xu, L.4    Kong, X.5    Li, Y.6    Dan, L.7    Hou, T.8
  • 8
    • 84945475267 scopus 로고    scopus 로고
    • Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening
    • [CrossRef][PubMed]
    • 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.[CrossRef][PubMed]
    • (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
  • 9
    • 85018596195 scopus 로고    scopus 로고
    • Structural and sequence similarity makes a significant impact on machine-learning-based scoring functions for protein–ligand interactions
    • [CrossRef][PubMed]
    • Li, Y.; Yang, J. Structural and sequence similarity makes a significant impact on machine-learning-based scoring functions for protein–ligand interactions. J. Chem. Inf. Model. 2017, 57, 1007–1012.[CrossRef][PubMed]
    • (2017) J. Chem. Inf. Model , vol.57 , pp. 1007-1012
    • Li, Y.1    Yang, J.2
  • 10
    • 66149103553 scopus 로고    scopus 로고
    • Comparative assessment of scoring functions on a diverse test Set
    • [CrossRef][PubMed]
    • 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.[CrossRef][PubMed]
    • (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
  • 11
    • 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
    • [CrossRef][PubMed]
    • 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. Inform. 2015, 34, 115–126.[CrossRef][PubMed]
    • (2015) Mol. Inform , vol.34 , pp. 115-126
    • Li, H.1    Leung, K.-S.2    Wong, M.-H.3    Ballester, P.J.4
  • 12
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • [CrossRef]
    • Breiman, L. Random forests. Mach. Learn. 2001, 45, 5–32.[CrossRef]
    • (2001) Mach. Learn , vol.45 , pp. 5-32
    • Breiman, L.1
  • 13
    • 84906829436 scopus 로고    scopus 로고
    • Substituting random forest for multiple linear regression improves binding affinity prediction of scoring functions: Cyscore as a case study
    • [CrossRef][PubMed]
    • Li, H.; Leung, K.-S.; Wong, M.-H.; Ballester, P.J. Substituting random forest for multiple linear regression improves binding affinity prediction of scoring functions: Cyscore as a case study. BMC Bioinform. 2014, 15, 291.[CrossRef][PubMed]
    • (2014) BMC Bioinform , vol.15 , pp. 291
    • Li, H.1    Leung, K.-S.2    Wong, M.-H.3    Ballester, P.J.4
  • 14
    • 84868679998 scopus 로고    scopus 로고
    • Machine learning scoring functions based on random forest and support vector regression
    • Ballester, P.J. Machine learning scoring functions based on random forest and support vector regression. Lect. Notes Bioinform. 2012, 7632, 14–25.
    • (2012) Lect. Notes Bioinform , vol.7632 , pp. 14-25
    • Ballester, P.J.1
  • 15
    • 84938280812 scopus 로고    scopus 로고
    • Low-quality structural and interaction data improves binding affinity prediction via random forest
    • [CrossRef][PubMed]
    • Li, H.; Leung, K.-S.; Wong, M.-H.; Ballester, P. Low-quality structural and interaction data improves binding affinity prediction via random forest. Molecules 2015, 20, 10947–10962.[CrossRef][PubMed]
    • (2015) Molecules , vol.20 , pp. 10947-10962
    • Li, H.1    Leung, K.-S.2    Wong, M.-H.3    Ballester, P.4
  • 16
    • 85008692166 scopus 로고    scopus 로고
    • CSM-lig: A web server for assessing and comparing protein–small molecule affinities
    • [CrossRef][PubMed]
    • Pires, D.E.V.; Ascher, D.B. CSM-lig: A web server for assessing and comparing protein–small molecule affinities. Nucl. Acids Res. 2016, 44, W557–W561.[CrossRef][PubMed]
    • (2016) Nucl. Acids Res , vol.44 , pp. W557-W561
    • Pires, D.E.V.1    Ascher, D.B.2
  • 17
    • 85044292918 scopus 로고    scopus 로고
    • Combining SFCscore with Random Forests leads to improved affinity prediction for protein–ligand complexes
    • Zilian, D.; Sotriffer, C.A. Combining SFCscore with Random Forests leads to improved affinity prediction for protein–ligand complexes. J. Cheminform. 2013, 5, P27.
    • (2013) J. Cheminform , vol.5 , pp. 27
    • Zilian, D.1    Sotriffer, C.A.2
  • 18
    • 78649517318 scopus 로고    scopus 로고
    • Leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets
    • [CrossRef][PubMed]
    • 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.[CrossRef][PubMed]
    • (2010) J. Chem. Inf. Model , vol.50 , pp. 1961-1969
    • Kramer, C.1    Gedeck, P.2
  • 19
    • 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
    • [CrossRef][PubMed]
    • 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.[CrossRef][PubMed]
    • (2011) J. Chem. Inf. Model , vol.51 , pp. 1739-1741
    • Ballester, P.J.1    Mitchell, J.B.O.2
  • 20
    • 84908242076 scopus 로고    scopus 로고
    • Beware of machine learning-based scoring functions-on the danger of developing black boxes
    • [CrossRef][PubMed]
    • 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.[CrossRef][PubMed]
    • (2014) J. Chem. Inf. Model , vol.54 , pp. 2807-2815
    • Gabel, J.1    Desaphy, J.2    Rognan, D.3
  • 21
    • 82355186299 scopus 로고    scopus 로고
    • NNScore 2.0: A neural-network receptor–ligand scoring function
    • Durrant, J.D.; McCammon, J.A. NNScore 2.0: A neural-network receptor–ligand scoring function. J. Chem. Inf. Model. 2011, 51, 2897–2903.
    • (2011) J. Chem. Inf. Model , vol.51 , pp. 2897-2903
    • Durrant, J.D.1    McCammon, J.A.2
  • 22
    • 84961761189 scopus 로고    scopus 로고
    • Novel scoring based distributed protein docking application to improve enrichment
    • [CrossRef][PubMed]
    • Pradeep, P.; Struble, C.; Neumann, T.; Sem, D.S.; Merrill, S.J. A novel scoring based distributed protein docking application to improve enrichment. IEEE/ACM Trans. Comput. Biol. Bioinform. 2015, 12, 1464–1469.[CrossRef][PubMed]
    • (2015) IEEE/ACM Trans. Comput. Biol. Bioinform , vol.12 , pp. 1464-1469
    • Pradeep, P.1    Struble, C.2    Neumann, T.3    Sem, D.S.4    Merrill, S.5
  • 23
    • 84986915838 scopus 로고    scopus 로고
    • Enhancing scoring performance of docking-based virtual screening through machine learning
    • [CrossRef]
    • Silva, G.C.; Simoes, C.J.V.; Carreiras, P.; Brito, R.M.M. enhancing scoring performance of docking-based virtual screening through machine learning. Curr. Bioinform. 2016, 11, 408–420.[CrossRef]
    • (2016) Curr. Bioinform , vol.11 , pp. 408-420
    • Silva, G.C.1    Simoes, C.J.V.2    Carreiras, P.3    Brito, R.4
  • 24
    • 85000454204 scopus 로고    scopus 로고
    • Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest
    • [CrossRef][PubMed]
    • Wang, C.; Zhang, Y. Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest. J. Comput. Chem. 2017, 38, 169–177.[CrossRef][PubMed]
    • (2017) J. Comput. Chem , vol.38 , pp. 169-177
    • Wang, C.1    Zhang, Y.2
  • 25
    • 85008475964 scopus 로고    scopus 로고
    • Boosting docking-based virtual screening with deep learning
    • [CrossRef][PubMed]
    • 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.[CrossRef][PubMed]
    • (2016) J. Chem. Inf. Model , vol.56 , pp. 2495-2506
    • Pereira, J.C.1    Caffarena, E.R.2    Dos Santos, C.N.3
  • 26
    • 85027440798 scopus 로고    scopus 로고
    • Performance of machine-learning scoring functions in structure-based virtual screening
    • [CrossRef][PubMed]
    • Wójcikowski, M.; Ballester, P.J.; Siedlecki, P. Performance of machine-learning scoring functions in structure-based virtual screening. Sci. Rep. 2017, 7, 46710.[CrossRef][PubMed]
    • (2017) Sci. Rep , vol.7 , pp. 46710
    • Wójcikowski, M.1    Ballester, P.J.2    Siedlecki, P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.