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 19 of 19 for “"Computational Docking"”.
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Computational Approaches For Designing Protein/inhibitor Complexes And Membrane Protein Variants
… aspect of the process. In this thesis, I use computational and experimental approaches to explore the most fundamental aspect of drug discovery: the molecular interactions of small-molecules inhibitors with proteins. In Part I (Chapters I and II), I describe how computational docking …
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The HIV-1 entry inhibition capabilities of Isoflavones
… potential drug targets were hypothesised using computational docking studies. All the Isoflavones were shown to inhibit HIV replication in the lower micromolar regions with IC50 values ranging from 6.2 to 10.6 μM. Two of the isoflavones, B and C, were shown to possess significant entry …
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Engineering a highly enantioselective horseradish peroxidase by directed evolution
… enantioselectivity, which were rationalized by computational docking studies.
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Refinement of the Docking Component of Virtual Screening for PPAR
… that bind to PPAR" (i.e. binders) using computational docking methods has proven difficult given the large binding cavity of the protein, which yields a large target area and variations in ligand positions within the binding site. We applied a combined computational and experimental …
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Phytochemical Investigation of Psychoactive Medicinal Plants for the Treatment of Neurological Disorders
… acacetin analogs were designed with the aid of computational docking studies, to improve their selectivity towards MAO-B. The structures of the isolated compounds were determined on the basis of HR-MS and 1D- and 2D-NMR studies; configurations were partly established by ECD calculations. …
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Characterization of Triggerable Quinones for the Development of Enzyme-Responsive Liposomes
… (kcat), enzyme efficiency (kcat/Km)) and computational docking studies for a series of quinone derivatives against hNQO1, and (3) preparation of quinone-based liposomes and evaluation in the presence of the different components included in an hNQO1 assay. Structural alterations on the …
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Computational modeling of protein-protein and protein-peptide interactions
… analysis. Therefore, it is important to develop computational docking methods that start from the structures of component proteins and predict the structure of their complexes, preferably with accuracy close to that provided by X-ray crystallography. This thesis details three applications of …
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Computationally and Experimentally Exploring the Type IV Pilus Assembly ATPase for Antivirulence Drug Discovery
… by ATP hydrolysis. The thesis work here explores computational and experimental methods for the discovery of antivirulence therapeutics targeting the T4P assembly ATPase PilB. A computational model of Chloracidobacterium thermophilum PilB was generated by homology modeling and molecular docking …
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Evaluation of new biorecognition elements for environmental monitoring
… lccβ laccase of T. versicolor. A combination of computational docking (SwissDock) and molecular biology techniques was used to generate rationally engineered laccases with increased ability to process large and persistent PAHs. These mutated isoforms were produced by heterologous expression in P. …
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Study of Dynamics on the Interfaces of Carbon-Based Nanomaterials and Nanobiosensor
… the power of molecular dynamics simulation and computational docking to analyze the dynamics at various nano-interfaces including graphene amphiphilic Janus nanosheet (AJN), carbon nanotubes (CNTs), and CNT array biosensor. Rational design of the functional interface is explored by comparison of …
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Computational studies of biomolecules to explore potential therapeutics for COVID-19 and SAMD9- associated diseases
… shown some degree of success. Advancements in computational methods have offered an excellent opportunity to explore biological macromolecule conformations, functions, and pathogenesis. Therefore, an in silico molecular docking and dynamics approach were used to search for interactions of 26 …
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Biochemical and Molecular Assessment of Toxicity of Primaquine Metabolites on Erythrocytes
… the hemotoxic response of PQ metabolites. The computational docking studies suggested stronger interactions of PQ metabolites with NQO2 compared to melatonin (the NQO2 inhibitor) and menadione (the NQO2 substrate). Together these results suggest that NQO2 might have a protective role against …
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Structural investigations of adenosylcobalamin-dependent enzyme maturation
… C. metallidurans ATR and use this structure in computational docking studies with C. metallidurans IcmF to probe the potential interfaces within a G-protein:ATR:mutase complex. Overall, this work deepens our understanding of the function of G-protein chaperones in the maturation of …
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Analyzing Resistance to Design Chemical Inhibitors of AAA Proteins
… enzymatic activity. These analyses, along with computational docking, can guide optimization of inhibitor potency and selectivity. We used this approach to design the pyrazolylpyrrolopyrimidine-based spastazoline - the first potent and selective chemical probe for spastin, a microtubule-severing …
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Structure, function and inhibition of GcpE, FPPS and GGPPS: targeting isoprenoid biosynthesis for drug discovery
… as an AA*B monomer and we propose using computational modeling and electron microscopy that the A* insert domain has a TIM barrel structure that interacts with the A domain. This structural arrangement enables the A and B domains to interact in a “cup and ball” manner during catalysis, …
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Predicting the Pose of β-Casomorphin-5 and 7 in the Opioid Receptors
… the crystal structures of these three receptors, computational molecular docking studies were done using the software GOLD to determine the conformation of β-casomorphin-5 and 7 when they bind to these three opioid receptors. GOLD was able to discriminate among the three receptors when docking the …
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Targeting Alternative Conformational States of the HIV-1 Rev Response Element Stem IIB using Small Molecules
… to discover small molecules binding to RRE using computational and experimental drug screening. </p><p>First, nuclear magnetic resonance (NMR) techniques are applied to identify the native and non-native conformations of RREIIB. Including relaxation dispersion NMR and a new strategy for directly …
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Exploring reactivity and component interactions in Toluene/o-Xylene Monooxygenase from pseudomonas sp. OX1
… concentration of ToMOC. Protein-binding studies, computational docking, and rapid electron transfer kinetics indicate that this inhibitory function results from competition between ToMOD and ToMOC for binding to ToMOH. These results are discussed in the context of additional proteins in the …
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Approaches for Enhancing Therapeutic Efficacy of a Novel IL-10 Gene Family Member: MDA-7/IL-24
… magnetic resonance (NMR) binding assays and computational docking studies, we have recently identified a series of new Apogossypol derivatives, compound 3 (BI-79D10) and compound 11 (BI-97C1), with pan-Bcl-2- inhibitory potency. BI-79D10 binds to Bcl- xL, Bcl-2, and Mcl-1 with IC50 values of …