Molegro Virtual Docker - References
Docking Algorithm
Molegro Virtual Docker uses the MolDock docking engine to predict ligand - protein interactions. MolDock is based on a new hybrid search algorithm, called guided differential evolution.
The guided differential evolution algorithm combines the differential evolution (DE) optimization technique with a cavity prediction algorithm which is dynamically used during the docking process.
Differential evolution was introduced by Storn and Price [1] in 1995 and has previously been applied to various optimization problems with great succes.
The use of predicted cavities during the search process allows for a fast and accurate identification of potential binding modes.
The MolDock docking engine has been benchmarked and is described in details in MolDock: A New Technique for High-Accuracy Molecular Docking (Journal of Medicinal Chemistry).
| Docking Product | Accuracy |
|---|
| Molegro Virtual Docker | 87.0% |
| Glide | 81.8% |
| Surflex | 75.3% |
| FlexX[*] | 57.9% |
Table 1: Accuracy of selected docking programs. A binding mode is regarded as correctly identified if the RMSD (to the native co-crystallized ligand) is less than 2.0Å. Before docking the ligands were energy minimized and randomized and all water molecules were removed from the complex. The dataset consists of the 77 complexes from the Surflex set as defined in Friesner et al. [2].
[*] Based on 76 out of the 77 complexes in the Surflex77 set.
[1] Storn, R.; Price, K.
Differential Evolution - A Simple And Efficient Adaptive Scheme for Global Optimization over Continuous Spaces.
Tech-report, International Computer Science Institute, Berkley, 1995.
[2] Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.
Glide: A New Approach for Rapid Accurate Docking And Scoring. 1. Method And Assessment of Docking Accuracy.
J. Med. Chem. 2004, 47, 1739-1749.
[3] Gehlhaar, D. K.; Verkhivker, G.; Rejto, P. A.; Fogel, D. B.; Fogel, L. J.; Freer, S. T.
Docking Conformationally Flexible Small Molecules Into a Protein Binding Site Through Evolutionary Programming.
Proceedings of the Fourth International Conference on Evolutionary Programming 1995, 615-627.
Selected References
The following papers demonstrates how Molegro Virtual Docker has been used in various contexts.
2009
A Group Center Overlap Based Approach for ‘‘3D QSAR’’ Studies on TIBO Derivatives
Nitin S. Sapre, Swagata Gupta, Nilanjana Pancholi, Neelima Sapre
Journal of Computational Chemistry, April 30, 2009 Vol. 30(6): pp. 922-933.
Discovery of Potent Thermolysin Inhibitors Using Structure Based Virtual Screening and Binding Assays
Mahmud Tareq Hassan Khan, Ole-Martin Fuskevåg, and Ingebrigt Sylte
J. Med. Chem., 2009, 52 (1), pp 48–61
Studies on the molecular recognition between bioactive peptides and angiotensin-converting enzyme
A. S. Pina and A. C. A. Roque
J. Mol. Recognit. 2009; 22: 162–168
Synthesis of novel 1,4-benzoxazin-3-one derivatives as inhibitors against tyrosine kinases
Takahiro Honda, Takahiro Terao, Hiroyuki Aono, and Masakazu Ban
Bioorganic & Medicinal Chemistry, Volume 17, Issue 2, 15 January 2009, Pages 699-708
Comparative Molecular Docking of Antitrypanosomal Natural Products into Multiple Trypanosoma brucei Drug Targets
Ifedayo V. Ogungbe and William N. Setzer
Molecules 2009, 14, pp. 1513-1536
2008
Structure function studies on the active site of the coelenterazine-dependent luciferase from Renilla
Jongchan Woo, Matthew H. Howell and Albrecht G. von Arnim
Protein Sci. 2008 17: 725-735
Novel Steroid Receptor Phyto-Modulator Compound A Inhibits Growth and Survival of Prostate Cancer Cells
Alexander Yemelyanov, Jennifer Czwornog, Lajos Gera, Sonali Joshi, Robert T. Chatterton, Jr., and Irina Budunova
Cancer Res 2008; 68: (12). June 15, pp. 4763-4773
Effects of Antibiotics on Quorum Sensing in Pseudomonas aeruginosa
Mette E. Skindersoe, Morten Alhede, Richard Phipps, Liang Yang, Peter O. Jensen, Thomas B. Rasmussen,2 Thomas Bjarnsholt, Tim Tolker-Nielsen, Niels Høiby,3 and Michael Givskov
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, Oct. 2008, p. 3648–3663
Assessing ligand efficiencies using template-based molecular docking and Tabu-clustering on tetrahydroimidazo-[4,5,1-jk][1,4]-benzodiazepin-2(1H)-one and -thione (TIBO) derivatives as HIV-1RT inhibitors
Nitin S. Sapre, Swagata Gupta and Neelima Sapre
J. Chem. Sci., Vol. 120, No. 4, July 2008, pp. 395–404
Inhibitors of Bacillus anthracis acetohydroxyacid synthase
Satish Kalme, Chien Ngoc Pham, Vinaykumar Gedi, Dung Tien Le, Jung-Do Choi, Sung-Kun Kim, Moon-Young Yoona
Enzyme and Microbial Technology 43 (2008) 270–275
Homology Modeling of Wild-type, D516V, and H526L Mycobacterium Tuberculosis RNA Polymerase and Their Molecular Docking Study with Inhibitors
Daniela Josa, Elaine F. F. da Cunha, Teodorico C. Ramalho, Thais C. S. Souza, Melissa S. Caetano
Journal of Biomolecular Structure & Dynamics, Volume 25, Issue Number 4, (2008), pp. 373-376
In silico screening against wild-type and mutant Plasmodium falciparum dihydrofolate reductase
Gary B. Fogel, Mars Cheung, Eric Pittman David Hecht
Journal of Molecular Graphics and Modelling, Volume 26, Issue 7, April 2008, Pages 1145-1152
Novel anti-HIV cyclotriazadisulfonamide derivatives as modeled by ligand- and receptor-based approaches
Julia R. Pinheiro, Michelle Bitencourt, Elaine F. F. da Cunha, Teodorico C. Ramalho, and Matheus P. Freitas
Bioorganic & Medicinal Chemistry, Volume 16, Issue 4, 15 February 2008, Pages 1683-1690
Design, synthesis and in vitro antitumor activity of 4-aminoquinoline and 4-aminoquinazoline derivatives targeting EGFR tyrosine kinase
Khaled Abouzid, Samia Shouman
Bioorganic & Medicinal Chemistry 16 (2008) 7543–7551
Binding Mode Analysis of 2,4-diamino-5-methyl-5-deaza-6-substituted Pteridines with Mycobacterium tuberculosis and Human Dihydrofolate Reductases
Elaine F. F. da Cunha, Teodorico C. Ramalho, and Robert C. Reynolds
Journal of Biomolecular Structure & Dynamics, Volume 25, Issue Number 4, pp. 377-385, 2008
2007
Modeling the inhibition of quadruple mutant Plasmodium falciparum dihydrofolate reductase by pyrimethamine derivatives
Gary B. Fogel, Mars Cheung, Eric Pittman, David Hecht
Journal of Computer-Aided Molecular Design, vol. 22, issue 1, pp. 29-38, 2007
Identification of a Bis-guanylhydrazone [4,4-Diacetyldiphenylurea-bis(guanylhydrazone); NSC 109555] as a Novel Chemotype for Inhibition of Chk2 Kinase
Andrew G. Jobson, John H. Cardellina II, Dominic Scudiero, Sudhir Kondapaka, Hongliang Zhang, Hijoo Kim, Robert Shoemaker, and Yves Pommier
MOLECULAR PHARMACOLOGY,Vol. 72, No. 4 , 2007
Crystal Structure of Homo sapiens Kynureninase
Santiago Lima, Roman Khristoforov, Cory Momany, and Robert S. Phillips
Biochemistry, 2007, 46 (10), pp 2735–2744
Chemical synthesis and biological evaluation of a NAD(P)H:quinone oxidoreductase-1 – targeted tripartite quinone drug delivery system
Milene Volpato, Nathalie Abou-Zeid, Richard W. Tanner, Lee T. Glassbrook, James Taylor, Ian Stratford, Paul M. Loadman,Mohammed Jaffar,and Roger M. Phillips
Mol Cancer Ther 2007;6(12), 2007
The widely utilized brominated flame retardant tetrabromobisphenol A (TBBPA) is a potent inhibitor of the SERCA Ca2+ pump
Oluseye A. Ogunbayo and Francesco Michelangeli
Biochem J. 2007 December 15; 408(Pt 3): 407–415.
Computer modeling study of small molecule inhibitors of ubiquitin-activating enzyme (El)
Zengjian Hu, Yuangfang Ma, and William Southerland
In proceedings of: The 1st International Conference on Bioinformatics and Biomedical Engineering (ICBBE), 2007, pp. 84-85.
Docking and virtual screening of ACE inhibitory dipeptides
Are Hugo Pripp
European Food Research and Technology A, Volume 225, Numbers 3-4, July 2007 , pp. 589-592(4)
2006
First Structure of a Eukaryotic Phosphohistidine Phosphatase
Robert D. Busam, Ann-Gerd Thorsell, Alex Flores, Martin Hammarstrom, Camilla Persson, and B. Martin Hallberg
THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 281, NO. 45, pp. 33830 –33834, November 10, 2006
Menadione-induced Reactive Oxygen Species Generation via Redox Cycling Promotes Apoptosis of Murine Pancreatic Acinar Cells
David N. Criddle, Stuart Gillies, Heidi K. Baumgartner-Wilson, Mohammed Jaffar, Edwin C. Chinje, Sarah Passmore, Michael Chvanov, Stephanie Barrow, Oleg V. Gerasimenko, Alexei V. Tepikin, Robert Sutton, and Ole H. Petersen
THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 281, NO. 52, pp. 40485–40492, December 29, 2006