메뉴 건너뛰기




Volumn 7, Issue 1, 2015, Pages

Open Drug Discovery Toolkit (ODDT): A new open-source player in the drug discovery field

Author keywords

Machine learning; Programming; Receptor ligand interactions; Scoring function; Statistical methods; Toolkit; Virtual screening

Indexed keywords


EID: 84932194253     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/s13321-015-0078-2     Document Type: Article
Times cited : (149)

References (26)
  • 1
    • 84866262970 scopus 로고    scopus 로고
    • Chemoinformatics: A view of the field and current trends in method development
    • 1:CAS:528:DC%2BC38Xlt1Kksrs%3D
    • Vogt M, Bajorath J (2012) Chemoinformatics: a view of the field and current trends in method development. Bioorg Med Chem 20:5317-5323
    • (2012) Bioorg Med Chem , vol.20 , pp. 5317-5323
    • Vogt, M.1    Bajorath, J.2
  • 2
    • 84866241579 scopus 로고    scopus 로고
    • Early phase drug discovery: Cheminformatics and computational techniques in identifying lead series
    • 1:CAS:528:DC%2BC38Xht12jt7vN
    • Duffy BC, Zhu L, Decornez H, Kitchen DB (2012) Early phase drug discovery: cheminformatics and computational techniques in identifying lead series. Bioorg Med Chem 20:5324-5342
    • (2012) Bioorg Med Chem , vol.20 , pp. 5324-5342
    • Duffy, B.C.1    Zhu, L.2    Decornez, H.3    Kitchen, D.B.4
  • 6
    • 33749513370 scopus 로고    scopus 로고
    • Scoring functions for protein-ligand docking
    • 1:CAS:528:DC%2BD28XhtVamsLrE
    • Jain AN (2006) Scoring functions for protein-ligand docking. Curr Protein Pept Sci 7:407-420
    • (2006) Curr Protein Pept Sci , vol.7 , pp. 407-420
    • Jain, A.N.1
  • 7
    • 66149103553 scopus 로고    scopus 로고
    • Comparative assessment of scoring functions on a diverse test set
    • 1:CAS:528:DC%2BD1MXkt1aqtLg%3D
    • Cheng T, Li X, Li Y, Liu Z, Wang R (2009) Comparative assessment of scoring functions on a diverse test set. J Chem Inf Model 49:1079-1093
    • (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
  • 8
    • 82355186299 scopus 로고    scopus 로고
    • NNScore 2.0: A neural-network receptor-ligand scoring function
    • 1:CAS:528:DC%2BC3MXhtlGjtrnO
    • Durrant JD, McCammon JA (2011) NNScore 2.0: a neural-network receptor-ligand scoring function. J Chem Inf Model 51:2897-2903
    • (2011) J Chem Inf Model , vol.51 , pp. 2897-2903
    • Durrant, J.D.1    McCammon, J.A.2
  • 9
    • 77952825581 scopus 로고    scopus 로고
    • A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking
    • 1:CAS:528:DC%2BC3cXlt1Cjs78%3D
    • Ballester PJ, Mitchell JBO (2010) A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking. Bioinf Oxf Engl 26:1169-1175
    • (2010) Bioinf Oxf Engl , vol.26 , pp. 1169-1175
    • Ballester, P.J.1    Mitchell, J.B.O.2
  • 10
    • 84883250593 scopus 로고    scopus 로고
    • SFCscore(RF): A random forest-based scoring function for improved affinity prediction of protein-ligand complexes
    • 1:CAS:528:DC%2BC3sXot1Sqtrc%3D
    • Zilian D, Sotriffer CA (2013) SFCscore(RF): a random forest-based scoring function for improved affinity prediction of protein-ligand complexes. J Chem Inf Model 53:1923-1933
    • (2013) J Chem Inf Model , vol.53 , pp. 1923-1933
    • Zilian, D.1    Sotriffer, C.A.2
  • 11
    • 80054908338 scopus 로고    scopus 로고
    • VSDMIP 1.5: An automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface
    • 1:CAS:528:DC%2BC3MXht1KjtbrE
    • Cabrera ÁC, Gil-Redondo R, Perona A, Gago F, Morreale A (2011) VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface. J Comput Aided Mol Des 25:813-824
    • (2011) J Comput Aided Mol des , vol.25 , pp. 813-824
    • Cabrera Á.1    Gil-Redondo, R.2    Perona, A.3    Gago, F.4    Morreale, A.5
  • 12
    • 84893376538 scopus 로고    scopus 로고
    • DiSCuS: An open platform for (not only) virtual screening results management
    • Wójcikowski M, Zielenkiewicz P, Siedlecki P (2014) DiSCuS: an open platform for (not only) virtual screening results management. J Chem Inf Model 54:347-354
    • (2014) J Chem Inf Model , vol.54 , pp. 347-354
    • Wójcikowski, M.1    Zielenkiewicz, P.2    Siedlecki, P.3
  • 13
    • 84928540931 scopus 로고    scopus 로고
    • Cinfony-combining Open Source cheminformatics toolkits behind a common interface
    • O'Boyle NM, Hutchison GR (2008) Cinfony-combining Open Source cheminformatics toolkits behind a common interface. Chem Cent J 2:24
    • (2008) Chem Cent J , vol.2 , pp. 24
    • O'Boyle, N.M.1    Hutchison, G.R.2
  • 14
    • 79952595565 scopus 로고    scopus 로고
    • The NumPy Array: A structure for efficient numerical computation
    • van der Walt S, Colbert SC, Varoquaux G (2011) The NumPy Array: a structure for efficient numerical computation. Comput Sci Eng 13:22-30
    • (2011) Comput Sci Eng , vol.13 , pp. 22-30
    • Van Der Walt, S.1    Colbert, S.C.2    Varoquaux, G.3
  • 15
    • 13244266921 scopus 로고    scopus 로고
    • Lead- and drug-like compounds: The rule-of-five revolution
    • 1:CAS:528:DC%2BD2MXhtlSqsrg%3D
    • Lipinski CA (2004) Lead- and drug-like compounds: the rule-of-five revolution. Drug Discov Today Technol 1:337-341
    • (2004) Drug Discov Today Technol , vol.1 , pp. 337-341
    • Lipinski, C.A.1
  • 17
    • 77950571108 scopus 로고    scopus 로고
    • New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays
    • 1:CAS:528:DC%2BC3cXhsF2qsLw%3D
    • Baell JB, Holloway GA (2010) New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J Med Chem 53:2719-2740
    • (2010) J Med Chem , vol.53 , pp. 2719-2740
    • Baell, J.B.1    Holloway, G.A.2
  • 18
    • 70349932423 scopus 로고    scopus 로고
    • AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
    • 1:CAS:528:DC%2BD1MXht1GitrnK
    • Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS et al (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30:2785-2791
    • (2009) J Comput Chem , vol.30 , pp. 2785-2791
    • Morris, G.M.1    Huey, R.2    Lindstrom, W.3    Sanner, M.F.4    Belew, R.K.5    Goodsell, D.S.6
  • 19
    • 76149120388 scopus 로고    scopus 로고
    • AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
    • 1:CAS:528:DC%2BD1MXhsFGnur3O
    • 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
  • 20
    • 0028854034 scopus 로고
    • Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
    • 1:CAS:528:DyaK2MXjtVKlsbc%3D
    • Jones G, Willett P, Glen RC (1995) Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol 245:43-53
    • (1995) J Mol Biol , vol.245 , pp. 43-53
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 23
    • 0023751431 scopus 로고
    • Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins
    • 1:CAS:528:DyaL1cXltVCqsbs%3D
    • Cramer RD, Patterson DE, Bunce JD (1988) Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J Am Chem Soc 110:5959-5967
    • (1988) J Am Chem Soc , vol.110 , pp. 5959-5967
    • Cramer, R.D.1    Patterson, D.E.2    Bunce, J.D.3
  • 24
    • 0042171659 scopus 로고    scopus 로고
    • Editorial: Machine learning methods in QSAR modelling
    • 1:CAS:528:DC%2BD3sXmtFeksLg%3D
    • Schneider G, Downs G (2003) Editorial: machine learning methods in QSAR modelling. QSAR Comb Sci 22:485-486
    • (2003) QSAR Comb Sci , vol.22 , pp. 485-486
    • Schneider, G.1    Downs, G.2
  • 25
    • 34347372642 scopus 로고    scopus 로고
    • Support vector machine for SAR/QSAR of phenethyl-amines
    • 1:CAS:528:DC%2BD2sXnvFynsLY%3D
    • Niu B, Lu W, Yang S, Cai Y, Li G (2007) Support vector machine for SAR/QSAR of phenethyl-amines. Acta Pharmacol Sin 28:1075-1086
    • (2007) Acta Pharmacol Sin , vol.28 , pp. 1075-1086
    • Niu, B.1    Lu, W.2    Yang, S.3    Cai, Y.4    Li, G.5
  • 26
    • 84929141895 scopus 로고    scopus 로고
    • PDB-wide collection of binding data: Current status of the PDBbind database
    • Liu Z, Li Y, Han L, Li J, Liu J, Zhao Z, Nie W, Liu Y, Wang R (2015) PDB-wide collection of binding data: current status of the PDBbind database. Bioinformatics 31:405-412
    • (2015) Bioinformatics , vol.31 , pp. 405-412
    • Liu, Z.1    Li, Y.2    Han, L.3    Li, J.4    Zhao, Z.5    Nie, W.6    Liu, Y.7    Wang, R.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.