메뉴 건너뛰기




Volumn 20, Issue 6, 2015, Pages 9977-9993

DockBench: An integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations

Author keywords

Docking benchmark; Molecular docking; Structure based drug design; Virtual screening

Indexed keywords

CHECKPOINT KINASE 1; LIGAND; MOLECULAR LIBRARY; PROTEIN BINDING; PROTEIN KINASE; PROTEIN KINASE INHIBITOR;

EID: 84938276045     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules20069977     Document Type: Article
Times cited : (40)

References (43)
  • 2
    • 0030815956 scopus 로고    scopus 로고
    • A virtual screening approach applied to the search for trypanothione reductase inhibitors
    • Horvath, D. A virtual screening approach applied to the search for trypanothione reductase inhibitors. J. Med. Chem. 1997, 40, 2412-2423.
    • (1997) J. Med. Chem. , vol.40 , pp. 2412-2423
    • Horvath, D.1
  • 3
    • 84884254531 scopus 로고    scopus 로고
    • Virtual screening in drug design
    • Kortagere, S. Humana Press: Totowa, NJ, USA
    • Lill, M. Virtual screening in drug design. In In Silico Models for Drug Discovery; Kortagere, S., Ed.; Humana Press: Totowa, NJ, USA, 2013; Volume 993, pp. 1-12.
    • (2013) Silico Models for Drug Discovery , vol.993 , pp. 1-12
    • Lill, M.1
  • 4
    • 0037363598 scopus 로고    scopus 로고
    • Comparison of ranking methods for virtual screening in lead-discovery programs
    • Wilton, D.; Willett, P.; Lawson, K.; Mullier, G. Comparison of Ranking Methods for Virtual Screening in Lead-Discovery Programs. J. Chem. Inf. Model. 2003, 43, 469-474.
    • (2003) J. Chem. Inf. Model. , vol.43 , pp. 469-474
    • Wilton, D.1    Willett, P.2    Lawson, K.3    Mullier, G.4
  • 5
    • 8844263008 scopus 로고    scopus 로고
    • Docking and scoring in virtual screening for drug discovery: Methods and applications
    • Kitchen, D.B.; Decornez, H.; Furr, J.R.; Bajorath, J. Docking and scoring in virtual screening for drug discovery: Methods and applications. Nat. Rev. Drug Discov. 2004, 3, 935-949.
    • (2004) Nat. Rev. Drug Discov. , vol.3 , pp. 935-949
    • Kitchen, D.B.1    Decornez, H.2    Furr, J.R.3    Bajorath, J.4
  • 6
    • 84874445951 scopus 로고    scopus 로고
    • Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context
    • Houston, D.R.; Walkinshaw, M.D. Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context. J. Chem. Inf. Model. 2013, 53, 384-390.
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 384-390
    • Houston, D.R.1    Walkinshaw, M.D.2
  • 8
    • 84904979697 scopus 로고    scopus 로고
    • Alternative quality assessment strategy to compare performances of GPCR-Ligand docking protocols: The human adenosine A2A receptor as a case study
    • Ciancetta, A.; Cuzzolin, A.; Moro, S. Alternative Quality Assessment Strategy to Compare Performances of GPCR-Ligand Docking Protocols: The Human Adenosine A2A Receptor as a Case Study. J. Chem. Inf. Model. 2014, 54, 2243-2254.
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 2243-2254
    • Ciancetta, A.1    Cuzzolin, A.2    Moro, S.3
  • 9
    • 0030867582 scopus 로고    scopus 로고
    • Conservation of the Chk1 checkpoint pathway in mammals: Linkage of DNA damage to Cdk regulation through Cdc25
    • Sanchez, Y.; Wong, C.; Thoma, R.S.; Richman, R.; Wu, Z.; Piwnica-Worms, H.; Elledge, S.J. Conservation of the Chk1 checkpoint pathway in mammals: Linkage of DNA damage to Cdk regulation through Cdc25. Science 1997, 277, 1497-1501.
    • (1997) Science , vol.277 , pp. 1497-1501
    • Sanchez, Y.1    Wong, C.2    Thoma, R.S.3    Richman, R.4    Wu, Z.5    Piwnica-Worms, H.6    Elledge, S.J.7
  • 10
    • 0038418869 scopus 로고    scopus 로고
    • Chk1 and Chk2 kinases in checkpoint control and cancer
    • Bartek, J.; Lukas, J. Chk1 and Chk2 kinases in checkpoint control and cancer. Cancer Cell 2003, 3, 421-429.
    • (2003) Cancer Cell , vol.3 , pp. 421-429
    • Bartek, J.1    Lukas, J.2
  • 12
    • 84938254728 scopus 로고    scopus 로고
    • accessed on 25 May
    • MMs DockBench. Available online: http://mms.dsfarm.unipd.it/mmsdockbench.html (accessed on 25 May 2015).
    • (2015) MMs DockBench
  • 13
    • 0033954256 scopus 로고    scopus 로고
    • The protein data bank
    • Berman, H.M. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-242.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 16
    • 76149120388 scopus 로고    scopus 로고
    • AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
    • Trott, O.; Olson, A.J. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 2010, 31, 455-461.
    • (2010) J. Comput. Chem. , vol.31 , pp. 455-461
    • Trott, O.1    Olson, A.J.2
  • 18
    • 1642310340 scopus 로고    scopus 로고
    • Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
    • Halgren, T.A.; Murphy, R.B.; Friesner, R.A.; Beard, H.S.; Frye, L.L.; Pollard, W.T.; Banks, J.L. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening. J. Med. Chem. 2004, 47, 1750-1759.
    • (2004) J. Med. Chem. , vol.47 , pp. 1750-1759
    • Halgren, T.A.1    Murphy, R.B.2    Friesner, R.A.3    Beard, H.S.4    Frye, L.L.5    Pollard, W.T.6    Banks, J.L.7
  • 20
    • 33751358567 scopus 로고    scopus 로고
    • Plants: Application of ant colony optimization to structure-based drug design
    • Dorigo, M., Gambardella, L.M., Birattari, M., Martinoli, A., Poli, R., Stützle, T. Springer Berlin Heidelberg: Berlin, Heidelberg, Germany
    • Korb, O.; Stützle, T.; Exner, T.E. Plants: Application of ant colony optimization to structure-based drug design. In Ant Colony Optimization and Swarm Intelligence; Dorigo, M., Gambardella, L.M., Birattari, M., Martinoli, A., Poli, R., Stützle, T., Eds.; Springer Berlin Heidelberg: Berlin, Heidelberg, Germany, 2006; Volume 4150, pp. 247-258.
    • (2006) Ant Colony Optimization and Swarm Intelligence , vol.4150 , pp. 247-258
    • Korb, O.1    Stützle, T.2    Exner, T.E.3
  • 21
    • 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
  • 22
    • 84855757480 scopus 로고    scopus 로고
    • 09. Chemical Computing Group Inc.: 1010 Sherbooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7, 2015
    • Molecular Operating Environment (MOE), 2014.09. Chemical Computing Group Inc.: 1010 Sherbooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7, 2015.
    • (2014) Molecular Operating Environment (MOE)
  • 24
    • 84885406698 scopus 로고    scopus 로고
    • GNU parallel-The command-line power tool
    • Tange, O. GNU Parallel-The Command-Line Power Tool. Login USENIX Mag. 2015, 36, 42-47.
    • (2015) Login USENIX Mag. , vol.36 , pp. 42-47
    • Tange, O.1
  • 25
    • 84938245734 scopus 로고    scopus 로고
    • Cambridge Crystallographic Data Centre: 12 Union Road, Cambridge CB2 1EZ, UK
    • GOLD suite, version 5.2; Cambridge Crystallographic Data Centre: 12 Union Road, Cambridge CB2 1EZ, UK.
    • GOLD Suite, Version 5.2
  • 26
    • 0037571112 scopus 로고    scopus 로고
    • Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
    • Halgren, T.A. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. J. Comput. Chem. 1996, 17, 490-519.
    • (1996) J. Comput. Chem. , vol.17 , pp. 490-519
    • Halgren, T.A.1
  • 36
    • 2242421834 scopus 로고    scopus 로고
    • Structural basis for Chk1 inhibition by UCN-01
    • Zhao, B. Structural Basis for Chk1 Inhibition by UCN-01. J. Biol. Chem. 2002, 277, 46609-46615.
    • (2002) J. Biol. Chem. , vol.277 , pp. 46609-46615
    • Zhao, B.1
  • 38
    • 84862282465 scopus 로고    scopus 로고
    • Discovery of Checkpoint Kinase Inhibitor (S)-5-(3-Fluorophenyl)-N-(piperidin-3-yl)-3-ureidothiophene-2-carboxamide (AZD7762) by Structure-Based Design and Optimization of Thiophenecarboxamide Ureas
    • Oza, V.; Ashwell, S.; Almeida, L.; Brassil, P.; Breed, J.; Deng, C.; Gero, T.; Grondine, M.; Horn, C.; Ioannidis, S.; et al. Discovery of Checkpoint Kinase Inhibitor (S)-5-(3-Fluorophenyl)-N-(piperidin-3-yl)-3-ureidothiophene-2-carboxamide (AZD7762) by Structure-Based Design and Optimization of Thiophenecarboxamide Ureas. J. Med. Chem. 2012, 55, 5130-5142.
    • (2012) J. Med. Chem. , vol.55 , pp. 5130-5142
    • Oza, V.1    Ashwell, S.2    Almeida, L.3    Brassil, P.4    Breed, J.5    Deng, C.6    Gero, T.7    Grondine, M.8    Horn, C.9    Ioannidis, S.10
  • 40
    • 65249157397 scopus 로고    scopus 로고
    • Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures
    • Labute, P. Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures. Proteins 2009, 75, 187-205.
    • (2009) Proteins , vol.75 , pp. 187-205
    • Labute, P.1
  • 41
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang, J.; Cieplak, P.; Kollman, P.A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 2000, 21, 1049-1074.
    • (2000) J. Comput. Chem. , vol.21 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 42
    • 84988129057 scopus 로고
    • Optimization of parameters for semiempirical methods I
    • Stewart, J.J.P. Optimization of parameters for semiempirical methods I. Method. J. Comput. Chem. 1989, 10, 209-220.
    • (1989) Method. J. Comput. Chem. , vol.10 , pp. 209-220
    • Stewart, J.J.P.1
  • 43
    • 84988073214 scopus 로고
    • Optimization of parameters for semiempirical methods II. Applications
    • Stewart, J.J.P. Optimization of parameters for semiempirical methods II. Applications. J. Comput. Chem. 1989, 10, 221-264.
    • (1989) J. Comput. Chem. , vol.10 , pp. 221-264
    • Stewart, J.J.P.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.