Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 18 of 18 for “"autodock"”.
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Improving Protein Docking Using Efficient Sustainable Evolutionary Algorithm
<p>AutoDock is a widely used automated protein docking program in structure-based drug-design. Different search algorithms, such as Simulated Annealing, traditional Genetic Algorithm and Lamarckian Genetic Algorithm are used in AutoDock. However, the docking performance of these algorithms is still …
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Structure-based approaches applied to the study of pharmaceutical relevant targets
… validation of covalent docking performed with Autodock.
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Autodocking Studies of Oxygenated Fullerenes as Inhibitors of The HIV Protease
… levels were studied via blind docking using AutoDock Vina software to elucidate the mechanism of these interactions. The structures of C60O, C60O2, C60O4, C60O6, C60O8 were generated using Spartan software and were docked with a crystal structure of the HIV-Protease (PR) obtained from The …
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Breast Cancer Progression and Phytoestrogen Interactions with Estrogen Receptors
… ligands (SWISS MODEL and docked through AutoDock Vina). Subsequently, isoforms of ERα and ERβ and different ligands (E1, E2, E3, PE, Tamoxifen, ICI 182,780) were modelled and tested by docking against the same set of ligands (E1, E2, E3, PE, Tamoxifen, ICI 182,780). The system described …
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Algorithms for Derivative-Free Optimization
… the state-of-the-art protein docking software AutoDock.
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Drug Repurposing for COVID-19 Using Molecular Docking Tools
… molecules with positive experimental results. AutoDock Vina was used to dock the molecules against the SARS-CoV-2 spike receptor bound to the ACE2 receptor (6M0J). Results were pre-filtered to 50 candidates according to their binding affinities and the 10 most promising molecules that have …
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Targeting RNA With Small Molecules: SL3 of HIV -1 Psi-Rna
… using sequentially the docking programs DOCK and AutoDock, followed by MD simulations. These studies revealed nine RNA ligands, four of which are selective for SL3 RNA. Chapter three describes how a combination of virtual screening and high-throughput screening strategies was used to identify SL3 …
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Structural investigation of 1,8-dinitro-4,5-dihydroxyanthraquinone and implications for docking as a small molecule inhibitor into the protease of West Nile virus
… it affects virtual screening efforts when using AutoDock as the structure-based docking program. It can be concluded that a stable tautomer does not exist in our crystal and that the conformation portrays a slight binding nature which could allude to a bent structure in polar solvents. …
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Biochemical and computational studies towards selective inhibition of the immunoproteasome
… molecular docking estimated binding energies. AutoDock and FRED simulations suggest increased β1i S1 pocket hydrophobicity, T21S and G97H substitutions from β1c to β1i as key towards favourable β1i binding. At β5c, small, hydrophobic characteristics of S2 become polar in β5i that enhances …
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Computational Molecular Docking Models and Design of Diarylpentanoids for the Androgen Receptor
… in MolSoft ICM Pro and further verified by AutoDock through 1-Click Docking. Further research into designing new ligands was performed however the results were inconclusive and needs further study.</p>
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Analysis of the biophysical and in silico exploration of the interaction between small ribonucleoprotein G and the RING finger domain of retinoblastoma binding protein 6 for the identification of protein anti-cancer compounds
… and characterisation of the proteins using Autodock Vina revealed the binding and interaction patterns of SNRPG with the RBBP6 RING Finger domain with a docking score of 3.40kcal/mol. Using I-TASSER, a potential inhibitor known as (2R)-2-[(2-methyl-5-phenylpyrazol-3-yl) carbonyl …
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Synthesis and biophysical evaluation of thiazole orange derivatives as DNA binding ligands
… of the effective derivatives were studied using AutoDock. Their inhibition of telomerase activities was studied using the TRAP assay. The cytotoxicity of these derivatives toward three cancer cell lines was also investigated using the MTS assay. The second part of this work focuses on development …
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The Structural Characterization and Bioactivity Assessment of Nonspecific Lipid Transfer Protein 1 (nsLTP1) from Caraway (Carum Carvi) Seeds
… structure was predicted using MODELLER and Autodock Vina software was employed for docking fatty acids against caraway nsLTP1. Assessment of nsLTP1 cytotoxic activity was achieved by MTS assay, and the Trolox equivalent antioxidant capacity (TAC) was determined. Secondary strucutre stability …
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Development of oxygenase biocatalysts for the production of synthetically useful cis-diol compounds
… putida UV4 but at a lower reaction rate. Using AutoDock (Vina), an analysis of the active site of TDO and its substrate interactions provided a rationale for earlier results and predicted new synthetically useful tricyclic cis-dihydrodiol metabolites. Molecular docking showed His311 and Gln215 …
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RNA recognition: controlling RNA-protein complexes with small molecules
… of 250,000 compounds and using the program AutoDock 3. Fluorescence and ITC experiments revealed that QD2 binds cooperatively to four identical binding sites on tGCAA RNA hairpin. The equilibrium binding dissociation constant of the four identical binding sites is 8.2 (±0.4) µM. CD …
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Integrated cellular, proteomic and metabolite analysis of argyrin B with rational design approaches for immunoproteasome-selective inhibitors
… sites were studied by molecular docking using Autodock 4.2. Results showed striking preferential binding at β1i site over β1c site (p<0.05) in 75% of analogues, with analogues K, J, I and B additionally exhibiting improved β5i over β5c binding (p<0.05). For further SAR insights, a panel of …
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Lead optimisation of dehydroemetine as an antimalarial option through drug repositioning and molecular modelling
… metronidazole treatment failure. Using MOE and Autodock vina docking software, the activities of two isomers of dehydroemetine; (-)-R,S-dehydroemetine and (-)-S,S-dehydroisoemetine were predicted. Docking studies predicted a better binding conformation for (-)-R,S-dehydroemetine compared to …
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Discovering Dengue Drugs-Together: Grid Scale Virtual Screening with Mean Field Free Energy of Binding Rescoring
The virtual screening of chemical databases against drug discovery targets with docking programs can enrich a database for bioactive compounds. However, current virtual screening methods generate many false positives leading to extensive and expensive testing of ultimately inactive compounds. In …