Molegro Virtual Docker - References
The MolDock docking engine used in Molegro Virtual Docker has been benchmarked and 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 (76 out of the 77 complexes) | 57.9% |
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. [J. Med. Chem. 2004, 47, 1739-1749].
Selected References
The following papers demonstrates how Molegro Virtual Docker has been used in various contexts.
2011
Identification of new potential Mycobacterium tuberculosis shikimate kinase inhibitors through molecular docking simulations
Journal of Molecular Modeling (early access)
Molecular and structural determinants of adamantyl susceptibility to HLA-DRs allelic variants: an in silico approach to understand the mechanism of MLEs
J Comput Aided Mol Des, 2011, 25:81-101
Bio-Inspired Algorithms Applied to Molecular Docking Simulations
Current Medicinal Chemistry, Volume 18, Number 9, March 2011, pp. 1339-1352
Biotin as acylating agent in the Friedel-Crafts reaction. Avidin affinity of biotinyl derivatives of ferrocene, ruthenocene and pyrene and fluorescence properties of 1-biotinylpyrene
Org. Biomol. Chem., 2011, Vol. 9, pp. 408-417
Docking study of HIV-1 reverse transcriptase with phytochemicals
Bioinformation 5(10), pp. 430-439, 2011
2010
Synthesis, Biological Activity, and Molecular Modeling Studies of 1H-1,2,3-Triazole Derivatives of Carbohydrates as α-Glucosidases Inhibitors
J. Med. Chem., 2010, 53 (6), pp. 2364-2375
De novo Based Ligand generation and Docking studies of PPARδ Agonists: Correlations between Predicted Biological activity vs. Biopharmaceutical Descriptors
Chem-Bio Informatics Journal, 2010, Vol.10, pp. 74-86
Docking of the alkaloid geissospermine into acetylcholinesterase: a natural scaffold targeting the treatment of Alzheimer's disease
JOURNAL OF MOLECULAR MODELING, Early Online
Design and synthesis of 2-quinolones as antioxidants and antimicrobials: a rational approach
Med Chem Res, 2010, Vol. 19, pp. 193-209
Concentration dependent effects of commonly used pesticides on activation versus inhibition of the quince (Cydonia Oblonga) polyphenol oxidase
Food and Chemical Toxicology, 2010, Vol. 48, pp. 957-963
In silico modeling of the specific inhibitory potential of thiophene-2,3-dihydro-1,5-benzothiazepine against BChE in the formation of β-amyloid plaques associated with Alzheimer's disease
Theoretical Biology and Medical Modelling 2010, 7:22
Evidences for antiosteoporotic and selective estrogen receptor modulator activity of silymarin compared with ethinylestradiol in ovariectomized rats
Phytomedicine, 2010, Vol. 17, pp. 116-125
Structural Basis of Membrane Targeting by the Dock180 Family of Rho Family Guanine Exchange Factors (Rho-GEFs)
J. Biol. Chem., 2010, Vol. 285, No. 17, pp. 13211-13222
MolDock Applied to Structure-Based Virtual Screening
Curr Drug Targets., 2010, Vol. 11, No. 3, pp. 327-34
Synthesis and Antimycobacterial Evaluation of Novel Phthalazin-4-ylacetamides Against log- and Starved Phase Cultures
Chem Biol Drug Des, 2010, Vol. 75, pp. 381-391
Structural Motifs and Biological Studies of New Antimony(III) Iodide Complexes with Thiones
Inorg. Chem., 2010, Vol. 49, pp. 488-501
Computational Investigation of the Anti-HIV Activity of Chinese Medicinal Formula Three-Huang Powder
Interdiscip Sci Comput Life Sci, 2010, Vol. 2, pp. 151-156
Cancer-relevant biochemical targets of cytotoxic Lonchocarpus flavonoids: A molecular docking analysis
J Mol Model, 2010, Vol. 16, pp. 311-326
Insights into antifolate activity of phytochemicals against Pseudomonas aeruginosa
Journal of Drug Targeting, 2010, Early Online
Computational analysis of the activity of pongachalcone I against highly resistant bacteria Pseudomonas putida
Bioinformation, 2010, Vol. 4, No. 10, pp. 473-477
Lead expansion and virtual screening of Indinavir derivate HIV-1 protease inhibitors using pharmacophoric - shape similarity scoring function
Bioinformation, 2010, Vol. 4, No. 7, pp. 295-299
Lead Optimization of Diarylpyrimidines as Non-nucleoside Inhibitors of HIV-1 Reverse Transcriptase
Chem Med Chem, 2010, Vol. 5, pp. 837-840
Synthesis, Antimicrobial Evaluation, and Docking Studies of Novel 4-Substituted Quinazoline Derivatives as DNA-Gyrase Inhibitors
Arch. Pharm. Chem. Life Sci., 2010, Vol. 10, pp. 570-576
Computer-Aided Design And Screening Of Chalcones As Novel PPAR Gamma Agonists
International Journal Of Pharmacy & Technology, 2010, Vol. 2, No.1, pp. 38-65
Evaluation of Enoyl-Acyl Carrier Protein Reductase Inhibitors as Pseudomonas aeruginosa Quorum-Quenching Reagents
Molecules, 2010, Vol. 15, pp. 780-792
In silico search for multi-target anti-inflammatories in Chinese herbs and formulas
Bioorganic & Medicinal Chemistry 18, 2010, pp. 2204-2218
Arachin derived peptides as selective angiotensin I-converting enzyme (ACE) inhibitors: Structure-activity relationship
Peptides 31, 2010, pp. 1165-1176
Surface plasmon resonance analysis of nuclear factor-κB protein interactions with the sesquiterpene lactone helenalin
Analytical Biochemistry 401, 2010, pp. 30-37
Crystallographic and docking studies of purine nucleoside phosphorylase from Mycobacterium tuberculosis
Bioorganic & Medicinal Chemistry 18, 2010, pp. 4769-4774
Tirucallic Acids Are Novel Pleckstrin Homology Domain-Dependent Akt Inhibitors Inducing Apoptosis in Prostate Cancer Cells
Mol Pharmacol, 77, pp. 378-387, 2010
Self-organizing molecular field analysis of 2,4-thiazolidinediones: A 3D-QSAR model for the development of human PTP1B inhibitors
European Journal of Medicinal Chemistry 45, 2010, pp. 2537-2546
Sulphonamides as Inhibitors of Protein Tyrosine Phosphatase 1B: A Three-Dimensional Quantitative Structure-Activity Relationship Study Using Self-Organizing Molecular Field Analysis Approach
Chem. Pharm. Bull. 58(4), pp. 526-532, 2010
Synthesis and Biological Evaluation of 3,6-diaryl-7H-thiazolo[3,2-b][1,2,4]triazin-7-one Derivatives as Acetylcholinesterase Inhibitors
Arch Pharm Res, Vol 33, No 10, pp. 1641-1649, 2010
Oxytocin-Gly-Lys-Arg: A Novel Cardiomyogenic Peptide
PLoS ONE 5(10): e13643, 2010
Discovery of novel anti-proliferative compounds against A549 cells by virtual screening
Chem-Bio Informatics Journal, Vol. 10, pp. 46-60
Pharmacophore modeling strategies for the development of novel nonsteroidal inhibitors of human aromatase (CYP19)
Bioorganic & Medicinal Chemistry Letters 20, 2010, pp. 3050-3064
Development of new acetylcholinesterase reactivators: Molecular modeling versus in vitro data
Chemico-Biological Interactions 185, 2010, pp. 73-77
Hybrid diarylbenzopyrimidine non-nucleoside reverse transcriptase inhibitors as promising new leads for improved anti-HIV-1 chemotherapy
Bioorganic & Medicinal Chemistry 18, 2010, pp. 5039-5047
Synthesis of some 5-phenylisoxazole-3-carboxylic acid derivatives as potent xanthine oxidase inhibitors
European Journal of Medicinal Chemistry 45, 2010, pp. 2663-2670
Therapeutic strategies underpinning the development of novel techniques for the treatment of HIV infection
Drug Discovery Today, Volume 15, Numbers 5/6, 2010, pp. 186-197
Structural studies of Helicase NS3 variants from Hepatitis C virus genotype 3 in virological sustained responder and non-responder patients
BMC Research Notes 2010, 3:196
Structure-Activity Relationships of GPR120 Agonists Based on a Docking Simulation
Mol Pharmacol 78, 2010, pp. 804-810
2009
A Group Center Overlap Based Approach for 3D QSAR Studies on TIBO Derivatives
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
J. Med. Chem., 2009, 52 (1), pp 48-61