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.
Results
Showing 1 to 9 of 9 for “"structural ensembles"”.
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Energy Landscaping - On the Relationship between Functionality and Sequence Mutations for Multifunctional Biomolecules
… where each funnel exhibits a distinct structural ensemble and function. This work explores how the principle of minimal frustration may be extended to multifunnel energy landscapes that are associated with multifunctional biomolecules. To achieve this aim, the computational potential …
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Weighting protein ensembles with Bayesian statistics and small-angle X-ray scattering data
… so their structures must be represented as ensembles. Typically, structural ensembles for IDPs are constructed by generating a set of conformations that yield ensemble averages that agree with pre-existing experimental data. However, as the number of experimental constraints is usually much …
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The conformational landscape of RNA translational regulators and their potential as drug discovery targets
… along a free-energy landscape. Knowledge of this structural landscape has become an important goal for understanding its diverse biological functions. In this case, NMR spectroscopy has emerged as an important player in the characterization of RNA structural ensembles, with solution-state …
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Accelerated simulations and computer-aided drug design of membrane proteins
… diseases (AD). Despite the importance, the structural dynamics and functional mechanisms of many membrane proteins remain poorly understood, which has greatly hindered effective drug design. Gaussian accelerated Molecular Dynamics (GaMD) is a novel technique that provides simultaneous …
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Investigating and Reprogramming RNA Folding with Molecular Probes
… and in many cases to switch among multiple structural states. Predicting and experimentally determining RNA structures remains challenging, particularly because of this propensity of one RNA sequence to form a heterogeneous ensemble of structures. This thesis investigates two related …
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Study of macromolecular interactions using computational solvent mapping
… peptide binding sites on proteins. Analyses of structural ensembles of ligand-free proteins using solvent mapping have shown that such ensembles contain pre-existing binding hot spots, and that such hot spots can be identified without any a priori knowledge of the ligand-bound structure. …
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Toward sequence-to-structure predictions of chromatin: Generative AI sheds light on genome organization
… data. ChromoGen provided biologically accurate structural ensembles throughout the genome of two cell types, including one omitted from its training data. This transferability suggests that ChromoGen can provide access to the organization of chromatin in a wide variety of cell types while only …
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Computational investigations of protein dynamics and its implication in cellular functions: two cases on membrane sculpting by protein complexes and molecular origin of Parkinson's disease
… model, PACE, to characterize in atomic detail structural ensembles of wild type and mutant monomeric α-synuclein in aqueous solution. The simulations reproduce structural properties of α-synuclein characterized in experiments, such as secondary structure content, long-range contacts, chemical …
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Small Molecule Binding to Disordered Proteins
… restrained with NMR data to identify the structural origins Aβ42's lower solubility with respect to Aβ40, and show how this structural insight can be applied towards novel therapeutic development targeting this disordered protein. In Chapter 4, using both experimental and computational …