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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 20 of 28 for “"protein-ligand interactions"”.
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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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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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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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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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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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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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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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Designing Compounds that Probe the Phosphatidylinositol 3-Kinase Signalosome
… is dedicated to investigating how specific protein-ligand interactions in the active site affect selectivity and affinity of inhibitors; how ATP-competitive inhibitors affect membrane binding of PI3Kα; how known membrane binding inhibitors of coagulation factor V and VIII C2 domains affect …
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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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Development and Application of a quantitative Mass spectrometry based Platform for Thermodynamic Analysis of Protein interaction Networks
<p>The identification and quantification of protein-protein interactions in large scale is critical to understanding biological processes at a systems level. Current approaches for the analysis of protein -protein interactions are generally not quantitative and largely limited to certain types of …
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Poly(phenylene ethynylene)s in biosensor applications
… PPEs were synthesized and used to probe interactions at the air-water interface. Subtle changes in the polymer structure could lead to great differences in protein-ligand interactions. The Langmuir technique offers a sensitive method for understanding the fundamental properties of PPEs.
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NMR, Crystallographic and Computational Investigations of Peptides, Proteins and Bisphosphonates: New Paradigms for Rational Drug Design
… and quantum chemistry to understand protein-ligand interactions, (2) employing computational modeling to gain insights into catalytic mechanisms and evolutionary origins of terpene synthases and cyclases, and finally (3) developing mathematical models based on enzyme-inhibition data …
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Affordable Quantum Chemistry via Data-Driven and Local Approximations to Non-Covalent Interactions
… physically-rooted insight into intermolecular interactions. A quantitative understanding of these interactions, in turn, is of crucial importance for chemical problems like the modeling of protein-ligand interactions or molecular crystals and clusters. Unfortunately, the expensive computational …
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Analysis of molecular interactions in the presence of side chain flexibility
Protein-protein and protein-ligand interactions are ubiquitous in biology. For many proteins, these interactions can be well simulated by assuming rigid body association, resulting in powerful predictions from protein-protein docking. These methods have also been applied to sample ensembles of …
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Improving Posing and Ranking of Molecular Docking
… projects and fundamental biological studies of protein-ligand interactions. Traditionally, molecular docking is used to address one of three following questions: (i) given a ligand molecule and a protein receptor, predict the binding mode (pose) of the ligand within the context of a receptor, …
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Computationally and Experimentally Exploring the Type IV Pilus Assembly ATPase for Antivirulence Drug Discovery
… the existing body of work and reveals important protein-ligand interactions and characteristics, particularly involving the ATP binding domain of PilB. This work supports the use of PilB in structure-based virtual screening to identify novel compounds targeting PilB. Additionally, through …
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Leveraging Local Perturbations to Map Allosteric Networks of Phosphatases
<p>Allostery is central to regulation of protein function, but our mechanistic understanding remains incomplete. A deeper understanding of how redistributions of conformational states drive allostery in proteins could allow us to better grasp natural regulatory principles in cells and open new …
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Computational approaches to predicting drug induced toxicity
… These were applied to the task of predicting protein-ligand interactions - including the prediction of hERG inhibition. Whilst, for some of the datasets considered, either ATUSR or USR-ATFP was found to perform marginally better than all other descriptor sets to which they were compared, most …
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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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