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Showing 1 to 20 of 90 for “"protein-ligand"”.
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Examination of Molecular Recognition in Protein-Ligand Interactions
… measurements to predict binding affinities of protein-ligand interactions. Collectively, my thesis research aimed to better understand the underlying driving forces and principles which govern molecular recognition and molecular design. A prospective study coupled computational predictions with …
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Untersuchungen von Protein-Ligand-Wechselwirkungen mit Hilfe von Computersimulationen
Protein-Ligand-Wechselwirkungen sind wichtige Phänomene der <br>Biochemie und an einer Vielzahl von Prozessen beteiligt, so <br>z.B. am Metabolismus, der Immunabwehr und der hormonellen <br>Signalübertragung. Die Wechselwirkung von Enzymen mit <br>Inhibitoren bildet die Basis der Wirkung vieler …
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Exploring Protein-Ligand Interaction with Rotamer-Library Based Refinement Tools
… extensively used for the predicting and refining protein sidechains, loops and tertiary structures. These refinement techniques have been expanded to allow the inclusion of protein-ligand interactions by developing and evaluating methods for creating rotamer libraries for small drug-like …
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Detection and analysis of binding sites and protein-ligand interactions
Detection and analysis of protein-ligand binding sites is an important area of research in drug discovery. The FTMap web server is an established computational method for detection of binding hot spots, or regions on the protein surface that contribute disproportionately to the ligand binding free …
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Free energy calculations of protein-ligand complexes with computational molecular dynamics
… Berechnung der freien Bindungsenergien von Protein-Ligand Komplexen ist ein Fachbereich, an dem starkes wissenschaftliches Interesse besteht. Die Präzision solcher Berechnungen der freien Energie für große Systeme, wie z.B. Proteine, mittels Molekulardynamik Simulationen mit atomarer …
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Molecular perspective of protein-ligand selectivity in host and parasitic plants
Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-12-01
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Probing human disease through protein-ligand and protein-lipid interactions via molecular simulation
Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-03-28 without embargo terms
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Application of hydrogen deuterium exchange mass spectrometry in protein-ligand and protein-protein interactions
Proteins are not static objects. They have a great variety of internal motions with different amplitudes and different timescales. These internal motions play an important role in catalytic processes. Therefore, the existence of an intimate relationship between protein dynamics and protein function …
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Towards more robust and efficient methods for the calculation of Protein-Ligand binding affinities
Biological processes often depend on protein-ligand binding events, so that accurate prediction of protein-ligand binding affinities is of central importance in structural based drug design. Although many techniques exist for calculating protein-ligand binding affinities, ranging from techniques …
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Protein-Ligand Binding Affinity Directed Multi-Objective Drug Design Based on Fragment Representation Methods
… by fragment-based drug search for a given protein target and the emergence of artificial intelligence (AI) approaches in this field, this work advances the field of in silico drug design by (1) integrating a graph fragmentation-based deep generative model with a deep evolutionary learning …
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STRUCTURE-BASED COMPUTATIONAL MODELING OF PROTEIN-LIGAND INTERACTIONS - APPLIED TO PROTEINS INVOLVED IN HUMAN DISEASES
Protein structure-based virtual screening of large chemical libraries is commonly performed against static X-ray and NMR structures. However, proteins are dynamic macromolecules occupying different conformational spaces. Consequently, different protein structures of the same protein could exhibit …
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Protein-ligand interaction studies and identification of new drug-like hits as cannabinoid receptor modulators
… the putative binding modes of Cannabis-derived ligands with CB1 and CB2 receptors, (2) the identification of novel CB1 inverse agonists, and (3) the identification of allosteric site(s) in the CB2 receptor and screening of new CB2 allosteric modulators (AMs).</p> <p>Chapter 1 describes …
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Application and Evaluation of a Chemical Modification- and Mass Spectrometry-Based Thermodynamic Assay for the Study of Protein-Ligand Interactions in Complex Mixtures
… studies. A protocol that could assay all the proteins in the proteome for both direct and indirect binding interactions of drugs would greatly facilitate studies of drug action. Recently, the SPROX (stability of proteins from rates of oxidation) technique was developed as a chemical …
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Synthesis of [beta]-heteroaryl propionates via trapping of carbocations with [pi]-nucleophiles, efforts towards the total synthesis of acutumine, and the design, synthesis, and thermodynamics of protein-ligand interactions at the Src SH2 domain
… behind the binding affinity of various ligands to the Src SH2 domain was also investigated. A series of four ligands were designed and enantioselectively synthesized in order to compare how differences in the conformations of the ligands affect the thermodynamics of binding. Namely, …
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Design, synthesis, and thermodynamic evaluation of peptidomimetic ligands binding to the Src SH2 domain
The ability to predict protein-ligand binding affinities is a difficult and elusive goal in the field of molecular recognition. Models exist to predict binding energetics; however, they are not always capable of considering the incidental events in ligand-binding due to the tendency of the Gibbs …
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Efficient Biomolecular Computations Towards Applications in Drug Discovery
… of this research is to improve the accuracy of protein-ligand binding calculations in the implicit solvent framework. To address the problem (1) GBNSR6, an accurate yet efficient flavor of GB, has been thoroughly explored in the context of protein-ligand binding, (2) a global multidimensional …
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Improving protein docking with binding site prediction
Protein-protein and protein-ligand interactions are fundamental as many proteins mediate their biological function through these interactions. Many important applications follow directly from the identification of residues in the interfaces between protein-protein and protein-ligand interactions, …
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COMPUTATIONAL APPROACHES FOR PROTEIN FOLDING AND LIGAND BINDING: FROM THERMODYNAMICS TO KINETICS
The cellular function of proteins, and their targeting by drug applications, are both governed by biomolecular thermodynamics and kinetics. In order to make meaningful and efficient predictions of these mechanisms, molecular simulations must be able to estimate the binding affinity and rates of …
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Development and Application of Covalent-Labeling Strategies for the Large-Scale Thermodynamic Analysis of Protein Folding and Ligand Binding
<p>Thermodynamic stability measurements on proteins and protein-ligand complexes can offer insights not only into the fundamental properties of protein folding reactions and protein functions, but also into the development of protein-directed therapeutic agents to combat disease. Conventional …
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The High Affinity Anti-Fluorescyl Immunoglobulin-M Response in Rabbits
… with other hapten systems. Characterization of protein-ligand interactions, solvent effects and the microenvironment of induced IgM antibody was feasible due to the spectral properties of fluorescein.
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