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Volumn 8, Issue 5, 2012, Pages

Accessible high-throughput virtual screening molecular docking software for students and educators

Author keywords

[No Author keywords available]

Indexed keywords

BUDGET CONTROL; DRUG THERAPY; GRAPHICAL USER INTERFACES; MOLECULAR BIOLOGY; MOLECULAR MODELING; THROUGHPUT;

EID: 84863705628     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002499     Document Type: Article
Times cited : (86)

References (41)
  • 2
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical free energy function
    • Morris G, Goodsell D, Halliday R, Huey R, Hart W, (1998) Automated docking using a Lamarckian genetic algorithm and an empirical free energy function. J Comput Chem 19: 1639-1662.
    • (1998) J Comput Chem , vol.19 , pp. 1639-1662
    • Morris, G.1    Goodsell, D.2    Halliday, R.3    Huey, R.4    Hart, W.5
  • 3
    • 0025135112 scopus 로고
    • Automated docking of substrates to proteins by simulated annealing
    • Goodsell DS, Olson AJ, (1990) Automated docking of substrates to proteins by simulated annealing. Proteins 8: 195-202.
    • (1990) Proteins , vol.8 , pp. 195-202
    • Goodsell, D.S.1    Olson, A.J.2
  • 4
    • 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, (2002) Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J Comput-Aided Mol Des 16: 11-26.
    • (2002) J Comput-Aided Mol Des , vol.16 , pp. 11-26
    • Wang, R.1    Lai, L.2    Wang, S.3
  • 5
    • 52049118327 scopus 로고    scopus 로고
    • MedusaScore: an accurate force field-based scoring function for virtual drug screening
    • Yin S, Biedermannova L, Vondrasek J, Dokholyan NV, (2008) MedusaScore: an accurate force field-based scoring function for virtual drug screening. J Chem Inf Model 48: 1656-1662.
    • (2008) J Chem Inf Model , vol.48 , pp. 1656-1662
    • Yin, S.1    Biedermannova, L.2    Vondrasek, J.3    Dokholyan, N.V.4
  • 6
    • 52249109585 scopus 로고    scopus 로고
    • DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0
    • Jiang X, Kumar K, Hu X, Wallqvist A, Reifman J, (2008) DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0. Chem Cent J 2: 18.
    • (2008) Chem Cent J , vol.2 , pp. 18
    • Jiang, X.1    Kumar, K.2    Hu, X.3    Wallqvist, A.4    Reifman, J.5
  • 7
    • 40749120187 scopus 로고    scopus 로고
    • DOVIS: an implementation for high-throughput virtual screening using AutoDock
    • Zhang S, Kumar K, Jiang X, Wallqvist A, Reifman J, (2008) DOVIS: an implementation for high-throughput virtual screening using AutoDock. BMC Bioinformatics 9: 185.
    • (2008) BMC Bioinformatics , vol.9 , pp. 185
    • Zhang, S.1    Kumar, K.2    Jiang, X.3    Wallqvist, A.4    Reifman, J.5
  • 8
    • 77952832378 scopus 로고    scopus 로고
    • VSDocker: a tool for parallel high-throughput virtual screening using AutoDock on Windows-based computer clusters
    • Prakhov ND, Chernorudskiy AL, Gainullin MR, (2010) VSDocker: a tool for parallel high-throughput virtual screening using AutoDock on Windows-based computer clusters. Bioinformatics 26: 1374-1375.
    • (2010) Bioinformatics , vol.26 , pp. 1374-1375
    • Prakhov, N.D.1    Chernorudskiy, A.L.2    Gainullin, M.R.3
  • 9
    • 76149120388 scopus 로고    scopus 로고
    • Software news and update AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
    • Trott O, Olson AJ, (2010) Software news and update 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
  • 10
    • 0033397980 scopus 로고    scopus 로고
    • Python: a programming language for software integration and development
    • Sanner MF, (1999) Python: a programming language for software integration and development. J Mol Graph Model 17: 57-61.
    • (1999) J Mol Graph Model , vol.17 , pp. 57-61
    • Sanner, M.F.1
  • 11
  • 12
    • 84872426377 scopus 로고    scopus 로고
    • DOVIS, version 2.0
    • Available:. Accessed December 2010
    • Jiang X, Kumar K, Hu X, Wallqvist A, Reifman J, (2008) DOVIS, version 2.0. Available: http://www.bioanalysis.org/downloads/DOVIS-2.0.1-installer.tar.gz. Accessed December 2010.
    • (2008)
    • Jiang, X.1    Kumar, K.2    Hu, X.3    Wallqvist, A.4    Reifman, J.5
  • 13
    • 13844312649 scopus 로고    scopus 로고
    • ZINC - A free database of commercially available compounds for virtual screening
    • Irwin JJ, Shoichet BK, (2004) ZINC - A free database of commercially available compounds for virtual screening. J Chem Inf Model 45: 177-182.
    • (2004) J Chem Inf Model , vol.45 , pp. 177-182
    • Irwin, J.J.1    Shoichet, B.K.2
  • 14
    • 79952528590 scopus 로고    scopus 로고
    • Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers
    • Collignon B, Schulz R, Smith JC, Baudry J, (2011) Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers. J Comp Chem 32: 1202-1209.
    • (2011) J Comp Chem , vol.32 , pp. 1202-1209
    • Collignon, B.1    Schulz, R.2    Smith, J.C.3    Baudry, J.4
  • 15
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ, (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 16
    • 2942619012 scopus 로고    scopus 로고
    • 3DCoffee: combining protein sequences and structures within multiple sequence alignments
    • O'Sullivan O, Suhre K, Abergel C, Higgins DG, Notredame C, (2004) 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J Mol Biol 340: 385-395.
    • (2004) J Mol Biol , vol.340 , pp. 385-395
    • O'Sullivan, O.1    Suhre, K.2    Abergel, C.3    Higgins, D.G.4    Notredame, C.5
  • 17
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell T, (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234: 779-815.
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.2
  • 18
    • 0033545622 scopus 로고    scopus 로고
    • ARTICLES - a general and fast scoring function for protein - ligand interactions: a simplified potential approach
    • Muegge I, Martin YC, (1999) ARTICLES- a general and fast scoring function for protein - ligand interactions: a simplified potential approach. J Med Chem 42: 791.
    • (1999) J Med Chem , vol.42 , pp. 791
    • Muegge, I.1    Martin, Y.C.2
  • 19
    • 0001704085 scopus 로고    scopus 로고
    • SCORE: a new empirical method for estimating the binding affinity of a protein-ligand complex
    • Wang R, Liu L, Lai L, Tang Y, (1998) SCORE: a new empirical method for estimating the binding affinity of a protein-ligand complex. J Mol Model 4: 379-394.
    • (1998) J Mol Model , vol.4 , pp. 379-394
    • Wang, R.1    Liu, L.2    Lai, L.3    Tang, Y.4
  • 20
    • 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 MD, Murray CW, Auton TR, Paolini GV, Mee RP, (1997) Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput-Aided Mol Des 11: 425-445.
    • (1997) J Comput-Aided Mol Des , vol.11 , pp. 425-445
    • Eldridge, M.D.1    Murray, C.W.2    Auton, T.R.3    Paolini, G.V.4    Mee, R.P.5
  • 21
    • 0028454828 scopus 로고
    • The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
    • Böhm HJ, (1994) The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput-Aided Mol Des 8: 243-256.
    • (1994) J Comput-Aided Mol Des , vol.8 , pp. 243-256
    • Böhm, H.J.1
  • 22
    • 17144383951 scopus 로고    scopus 로고
    • A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
    • Zhang C, Liu S, Zhu Q, Zhou Y, (2005) A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J Med Chem 48: 2325-2335.
    • (2005) J Med Chem , vol.48 , pp. 2325-2335
    • Zhang, C.1    Liu, S.2    Zhu, Q.3    Zhou, Y.4
  • 23
    • 77956802186 scopus 로고    scopus 로고
    • Computational investigation of the anti-HIV activity of Chinese medicinal formula three-Huang powder
    • Hu JZ, Bai L, Chen DG, Xu QT, Southerland WM, (2010) Computational investigation of the anti-HIV activity of Chinese medicinal formula three-Huang powder. Interdiscip Sci 2: 151-156.
    • (2010) Interdiscip Sci , vol.2 , pp. 151-156
    • Hu, J.Z.1    Bai, L.2    Chen, D.G.3    Xu, Q.T.4    Southerland, W.M.5
  • 24
    • 13044295993 scopus 로고    scopus 로고
    • Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: a platform for antiviral drug design
    • Goldgur Y, Craigie R, Cohen GH, Fujiwara T, Yoshinaga T, et al. (1999) Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: a platform for antiviral drug design. Proc Natl Acad Sci U S A 96: 13040-13043.
    • (1999) Proc Natl Acad Sci U S A , vol.96 , pp. 13040-13043
    • Goldgur, Y.1    Craigie, R.2    Cohen, G.H.3    Fujiwara, T.4    Yoshinaga, T.5
  • 25
    • 34548569065 scopus 로고    scopus 로고
    • WinDock: structure-based drug discovery on Windows-based PCs
    • Hu Z, Southerland W, (2007) WinDock: structure-based drug discovery on Windows-based PCs. J Comput Chem 28: 2347-2351.
    • (2007) J Comput Chem , vol.28 , pp. 2347-2351
    • Hu, Z.1    Southerland, W.2
  • 26
    • 33748173818 scopus 로고    scopus 로고
    • BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock
    • Vaqué M, Arola A, Aliagas C, Pujadas G, (2006) BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock. Bioinformatics 22: 1803-1804.
    • (2006) Bioinformatics , vol.22 , pp. 1803-1804
    • Vaqué, M.1    Arola, A.2    Aliagas, C.3    Pujadas, G.4
  • 27
    • 56449130948 scopus 로고    scopus 로고
    • Volatile anesthetic binding to proteins is influenced by solvent and aliphatic residues
    • Streiff JH, Jones KA, (2008) Volatile anesthetic binding to proteins is influenced by solvent and aliphatic residues. J Chem Inf Model 48: 2066-2073.
    • (2008) J Chem Inf Model , vol.48 , pp. 2066-2073
    • Streiff, J.H.1    Jones, K.A.2
  • 29
    • 79960642266 scopus 로고    scopus 로고
    • DockoMatic: Automated peptide analog creation for high throughput virtual screening
    • Jacob RB, Bullock CW, Andersen T, McDougal OM, (2011) DockoMatic: Automated peptide analog creation for high throughput virtual screening. J Comp Chem 32: 2936-2941.
    • (2011) J Comp Chem , vol.32 , pp. 2936-2941
    • Jacob, R.B.1    Bullock, C.W.2    Andersen, T.3    McDougal, O.M.4
  • 30
    • 0005994352 scopus 로고    scopus 로고
    • Properties of neuronal nicotinic acetylcholine receptors: Pharmacological characterization and modulation of synaptic function
    • Albuquerque EX, Alkondon M, Pereira EFR, Castro NG, Schrattenholz A, et al. (1997) Properties of neuronal nicotinic acetylcholine receptors: Pharmacological characterization and modulation of synaptic function. J Pharmacol Exp Ther 280: 1117-1136.
    • (1997) J Pharmacol Exp Ther , vol.280 , pp. 1117-1136
    • Albuquerque, E.X.1    Alkondon, M.2    Pereira, E.F.R.3    Castro, N.G.4    Schrattenholz, A.5
  • 31
    • 84857435303 scopus 로고    scopus 로고
    • digital briefs: New software and websites for the chemical enterprise
    • Wolf LK, (2009) digital briefs: New software and websites for the chemical enterprise. C&EN 87: 32.
    • (2009) C&EN , vol.87 , pp. 32
    • Wolf, L.K.1
  • 36
    • 84855626190 scopus 로고    scopus 로고
    • DockingServer
    • Virtua Drug Ltd, Available:. Accessed December 2010
    • Virtua Drug Ltd (2009) DockingServer. Available: http://www.dockingserver.com. Accessed December 2010.
    • (2009)
  • 37
    • 74049093947 scopus 로고    scopus 로고
    • Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock
    • Bikadi Z, Hazai E, (2009) Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock. J Cheminf 1: 15.
    • (2009) J Cheminf , vol.1 , pp. 15
    • Bikadi, Z.1    Hazai, E.2
  • 38
    • 77952335476 scopus 로고    scopus 로고
    • Role of basic residues within or near the predicted transmembrane helix 2 of the human breast cancer resistance protein in drug transport
    • Cai X, Bikadi Z, Ni Z, Lee E-W, Wang H, et al. (2010) Role of basic residues within or near the predicted transmembrane helix 2 of the human breast cancer resistance protein in drug transport. J Pharmacol Exp Ther 333: 670-681.
    • (2010) J Pharmacol Exp Ther , vol.333 , pp. 670-681
    • Cai, X.1    Bikadi, Z.2    Ni, Z.3    Lee, E.-W.4    Wang, H.5
  • 39
    • 78649692457 scopus 로고    scopus 로고
    • MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters
    • Abreu R, Froufe H, Queiroz M, Ferreira I, (2010) MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters. J Cheminf 2: 10.
    • (2010) J Cheminf , vol.2 , pp. 10
    • Abreu, R.1    Froufe, H.2    Queiroz, M.3    Ferreira, I.4
  • 40
    • 78449264099 scopus 로고    scopus 로고
    • The PyMOL molecular graphics system. Version 1.3 ed
    • Available:. Accessed 7 May 2012
    • Shrodinger LLC, (2009) The PyMOL molecular graphics system. Version 1.3 ed. Available: http://www.pymol.org. Accessed 7 May 2012.
    • (2009)
    • Shrodinger, L.L.C.1
  • 41
    • 11144229113 scopus 로고    scopus 로고
    • AutoDock Tools: virtual screening of human 5-aminoimidazole-4-carboxamide ribonucleotide transformylase against the NCI diversity set by use of AutoDock to identify novel nonfolate inhibitors
    • Li C, Xu L, Wolan D, Wilson L, Olson A, (2004) AutoDock Tools: virtual screening of human 5-aminoimidazole-4-carboxamide ribonucleotide transformylase against the NCI diversity set by use of AutoDock to identify novel nonfolate inhibitors. J Med Chem 47: 6881-6690.
    • (2004) J Med Chem , vol.47 , pp. 6690-6881
    • Li, C.1    Xu, L.2    Wolan, D.3    Wilson, L.4    Olson, A.5


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