메뉴 건너뛰기




Volumn 54, Issue 15, 2011, Pages 5422-5431

Docking performance of fragments and druglike compounds

Author keywords

[No Author keywords available]

Indexed keywords

AURORA A KINASE; BETA SECRETASE; CYCLIN DEPENDENT KINASE 2; FIBROBLAST GROWTH FACTOR RECEPTOR 1; HEAT SHOCK PROTEIN 90; INDUCIBLE NITRIC OXIDE SYNTHASE; JANUS KINASE 2; METHIONYL AMINOPEPTIDASE 2; PROTEIN KINASE B; SYNAPTOPHYSIN; UROKINASE;

EID: 79961241154     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/jm200558u     Document Type: Article
Times cited : (116)

References (45)
  • 2
    • 0028854034 scopus 로고
    • Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
    • Jones, G.; Willett, P.; Glen, R. C. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation J. Mol. Biol. 1995, 245, 43-53
    • (1995) J. Mol. Biol. , vol.245 , pp. 43-53
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 3
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • DOI 10.1006/jmbi.1996.0897
    • 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 (Pubitemid 27170693)
    • (1997) Journal of Molecular Biology , vol.267 , Issue.3 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 4
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • DOI 10.1006/jmbi.1996.0477
    • Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm J. Mol. Biol. 1996, 261, 470-489 (Pubitemid 26335901)
    • (1996) Journal of Molecular Biology , vol.261 , Issue.3 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 5
    • 79952262090 scopus 로고    scopus 로고
    • FRED pose prediction and virtual screening accuracy
    • McGann, M. FRED pose prediction and virtual screening accuracy J. Chem. Inf. Model. 2011, 51, 578-596
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 578-596
    • McGann, M.1
  • 6
    • 0037434582 scopus 로고    scopus 로고
    • Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine
    • DOI 10.1021/jm020406h
    • Jain, A. N. Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine J. Med. Chem. 2003, 46, 499-511 (Pubitemid 36182752)
    • (2003) Journal of Medicinal Chemistry , vol.46 , Issue.4 , pp. 499-511
    • Jain, A.N.1
  • 9
    • 84986522918 scopus 로고
    • ICM-a new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
    • Abagyan, R.; Totrov, M.; Kuznetsov, D. ICM-a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation J. Comput. Chem. 1994, 15, 488-506
    • (1994) J. Comput. Chem. , vol.15 , pp. 488-506
    • Abagyan, R.1    Totrov, M.2    Kuznetsov, D.3
  • 12
    • 33846933784 scopus 로고    scopus 로고
    • Optimizing fragment and scaffold docking by use of molecular interaction fingerprints
    • DOI 10.1021/ci600342e
    • Marcou, G.; Rognan, D. Optimizing fragment and scaffold docking by use of molecular interaction fingerprints J. Chem. Inf. Model. 2007, 47, 195-207 (Pubitemid 46237537)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.1 , pp. 195-207
    • Marcou, G.1    Rognan, D.2
  • 13
    • 49449086848 scopus 로고    scopus 로고
    • An alternative method for the evaluation of docking performance: RSR vs RMSD
    • Yusuf, D.; Davis, A. M.; Kleywegt, G. J.; Schmitt, S. An alternative method for the evaluation of docking performance: RSR vs RMSD J. Chem. Inf. Model. 2008, 48, 1411-1422
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 1411-1422
    • Yusuf, D.1    Davis, A.M.2    Kleywegt, G.J.3    Schmitt, S.4
  • 15
    • 77954036921 scopus 로고    scopus 로고
    • Virtual fragment docking by glide: A validation study on 190 protein-fragment complexes
    • Sandor, M.; Kiss, R.; Keseru, G. M. Virtual fragment docking by glide: a validation study on 190 protein-fragment complexes J. Chem. Inf. Model. 2010, 50, 1165-1172
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 1165-1172
    • Sandor, M.1    Kiss, R.2    Keseru, G.M.3
  • 16
    • 60549086155 scopus 로고    scopus 로고
    • Four-dimensional docking: A fast and accurate account of discrete receptor flexibility in ligand docking
    • Bottegoni, G.; Kufareva, I.; Totrov, M.; Abagyan, R. Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking J. Med. Chem. 2009, 52, 397-406
    • (2009) J. Med. Chem. , vol.52 , pp. 397-406
    • Bottegoni, G.1    Kufareva, I.2    Totrov, M.3    Abagyan, R.4
  • 21
    • 3042806401 scopus 로고    scopus 로고
    • A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
    • DOI 10.1002/prot.20088
    • Perola, E.; Walters, W. P.; Charifson, P. S. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance Proteins 2004, 56, 235-249 (Pubitemid 38850158)
    • (2004) Proteins: Structure, Function and Genetics , vol.56 , Issue.2 , pp. 235-249
    • Perola, E.1    Walters, W.P.2    Charifson, P.S.3
  • 22
    • 67650997041 scopus 로고    scopus 로고
    • Virtual fragment screening: An exploration of various docking and scoring protocols for fragments using Glide
    • Kawatkar, S.; Wang, H.; Czerminski, R.; Joseph-McCarthy, D. Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide J. Comput.-Aided Mol. Des 2009, 23, 527-539
    • (2009) J. Comput.-Aided Mol. des , vol.23 , pp. 527-539
    • Kawatkar, S.1    Wang, H.2    Czerminski, R.3    Joseph-Mccarthy, D.4
  • 23
    • 67651002876 scopus 로고    scopus 로고
    • Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation
    • Loving, K.; Salam, N. K.; Sherman, W. Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation J. Comput.-Aided Mol. Des 2009, 23, 541-554
    • (2009) J. Comput.-Aided Mol. des , vol.23 , pp. 541-554
    • Loving, K.1    Salam, N.K.2    Sherman, W.3
  • 27
    • 0141726877 scopus 로고    scopus 로고
    • A 'Rule of Three' for fragment-based lead discovery?
    • DOI 10.1016/S1359-6446(03)02831-9, PII S1359644603028319
    • Congreve, M.; Carr, R.; Murray, C.; Jhoti, H. A "rule of three" for fragment-based lead discovery? Drug Discovery Today 2003, 8, 876-877 (Pubitemid 37194496)
    • (2003) Drug Discovery Today , vol.8 , Issue.19 , pp. 876-877
    • Congreve, M.1    Carr, R.2    Murray, C.3    Jhoti, H.4
  • 28
    • 0031024171 scopus 로고    scopus 로고
    • Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
    • DOI 10.1016/S0169-409X(96)00423-1, PII S0169409X96004231
    • Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv. Drug Delivery Rev. 1997, 23, 3-25 (Pubitemid 27046991)
    • (1997) Advanced Drug Delivery Reviews , vol.23 , Issue.1-3 , pp. 3-25
    • Lipinski, C.A.1    Lombardo, F.2    Dominy, B.W.3    Feeney, P.J.4
  • 29
    • 84906455988 scopus 로고    scopus 로고
    • Daylight Chemical Information Systems Inc. Aliso Vieja, CA
    • Daylight; Daylight Chemical Information Systems Inc.: Aliso Vieja, CA, 2006; www.daylight.com.
    • (2006) Daylight
  • 30
    • 79961225748 scopus 로고    scopus 로고
    • Software from BioByte Corp. 201 W. 4th Street, No. 204, Claremont, CA 91711-4707
    • Software from BioByte Corp., 201 W. 4th Street, No. 204, Claremont, CA 91711-4707; 2006.
    • (2006)
  • 31
    • 31444452744 scopus 로고
    • Automatic generation of 3D-atomic coordinates for organic molecules
    • Gasteiger, J.; Rudolph, C.; Sadowski, J. Automatic generation of 3D-atomic coordinates for organic molecules Tetrahedron Comput. Methodol. 1990, 3, 537-547
    • (1990) Tetrahedron Comput. Methodol. , vol.3 , pp. 537-547
    • Gasteiger, J.1    Rudolph, C.2    Sadowski, J.3
  • 32
    • 0040196029 scopus 로고    scopus 로고
    • Further development of a genetic algorithm for ligand docking and its application to screening combinatorial libraries
    • Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Further Development of a Genetic Algorithm for Ligand Docking and Its Application to Screening Combinatorial Libraries. In Rational Drug Design: Novel Methodology and Practical Applications; Parrill, A. L.; Reddy, M. R., Eds.; American Chemical Society: Washington, DC, 1999; pp 271-291. (Pubitemid 129547006)
    • (1999) ACS Symposium Series , vol.719 , pp. 271-291
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 34
    • 0031226772 scopus 로고    scopus 로고
    • Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
    • Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. Empirical scoring functions. 1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes J. Comput.-Aided Mol. Des 1997, 11, 425-445 (Pubitemid 127505895)
    • (1997) Journal of Computer-Aided Molecular Design , vol.11 , Issue.5 , pp. 425-445
    • Eldridge, M.D.1    Murray, C.W.2    Auton, T.R.3    Paolini, G.V.4    Mee, R.P.5
  • 37
    • 62449330667 scopus 로고    scopus 로고
    • Empirical scoring functions for advanced protein-ligand docking with PLANTS
    • Korb, O.; Stützle, T.; Exner, T. E. Empirical scoring functions for advanced protein-ligand docking with PLANTS J. Chem. Inf. Model. 2009, 49, 84-96
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 84-96
    • Korb, O.1    Stützle, T.2    Exner, T.E.3
  • 39
    • 1842479952 scopus 로고    scopus 로고
    • Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model
    • DOI 10.1002/prot.20033
    • Onufriev, A.; Bashford, D.; Case, D. A. Exploring protein native states and large-scale conformational changes with a modified generalized born model Proteins 2004, 55, 383-394 (Pubitemid 38437495)
    • (2004) Proteins: Structure, Function and Genetics , vol.55 , Issue.2 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 41
    • 67650149263 scopus 로고    scopus 로고
    • QM/MM as a tool in fragment based drug discovery. A cross-docking, rescoring study of kinase inhibitors
    • Gleeson, M. P.; Gleeson, D. QM/MM as a tool in fragment based drug discovery. A cross-docking, rescoring study of kinase inhibitors J. Chem. Inf. Model. 2009, 49, 1437-1448
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1437-1448
    • Gleeson, M.P.1    Gleeson, D.2
  • 43
    • 78649505687 scopus 로고    scopus 로고
    • Docking validation resources: Protein family and ligand flexibility experiments
    • Mukherjee, S.; Balius, T. E.; Rizzo, R. C. Docking validation resources: protein family and ligand flexibility experiments J. Chem. Inf. Model. 2010, 50, 1986-2000
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 1986-2000
    • Mukherjee, S.1    Balius, T.E.2    Rizzo, R.C.3
  • 45
    • 1942453243 scopus 로고    scopus 로고
    • Ligand efficiency: A useful metric for lead selection
    • DOI 10.1016/S1359-6446(04)03069-7, PII S1359644604030697
    • Hopkins, A. L.; Groom, C. R.; Alex, A. Ligand efficiency: a useful metric for lead selection Drug Discovery Today 2004, 9, 430-431 (Pubitemid 38510559)
    • (2004) Drug Discovery Today , vol.9 , Issue.10 , pp. 430-431
    • Hopkins, A.L.1    Groom, C.R.2    Alex, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.