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Showing 1 to 10 of 10 for “"energy landscape theory"”.
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Physical models of protein folding within the energy landscape theory
The energy landscape theory of protein fol9.ing is based on a statistical description of a protein's complex potential energy surface. Individual folding events are sampled from an ensemble of possible routes on the landscape. The theory suggests that the landscape of a protein can be described as …
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Application of the Statistical Energy Landscape Theory to Protein Structure Prediction
… methods to narrow this gap. Using ideas from the energy landscape theory first introduced by Bryngelson and Wolynes, and database analysis, we have designed statistical mechanical energy functions for protein structure prediction by threading and simulated annealing molecular dynamics methods. …
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K-means landscapes: exploring clustering solution spaces using energy landscape theory
… performance. We present the application of energy landscape theory to the K-means cost function to elucidate its topography, which we deduce from K-means landscapes described in terms minima and transition states. We analyse K-means landscapes for Fisher’s Iris dataset, the glass …
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Applications of Funneled Landscapes: Protein Folding and Molecular Recognition
Energy landscape theory provides a general framework in which models can be used to describe complex macromolecular processes. A free energy functional model is formulated to describe protein folding which includes a specific potential, a polymer chain entropy, and explicit physically motivated …
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Studies of Protein-Protein and Protein-Water Interactions by Small Angle X-Ray Scattering, Terahertz Spectroscopy, ASMOS, And Computer Simulation
… in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very …
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On the role of conformational flexibility in viral fusion mechanisms - fusion by disorder
… distributions of the entire functional landscape through standard molecular dynamics calculations is not currently feasible. In this body of work, we employ structure based models to analyze the conformational dynamics of a range of viral fusion proteins. Structure based models have …
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Barrier Heights and Diffusion Coefficients in Protein Folding
… two-state, all-or-none transition. However, the energy landscape theory of protein folding predicts small and even zero folding free energy barriers (downhill folding) because of partial or complete compensation between large enthalpic and entropic terms as folding proceeds. They have been …
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Evolutionary Fitness of Non-Coding Genetic Elements
… amino acid sequences. We also discuss the energy landscape theory and the physical energy function-- the Associative Memory, Water Mediated, Structure and Energy Model (AWSEM)--informed by the theory's principles. We finally discuss the Direct Coupling Analysis (DCA) model, which, when used …
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Anaerobic, NADH-Dependent Haem Breakdown in a Family of Haemoproteins
… experimental methods were combined with Energy Landscape Theory. Deuterium labelling demonstrated that the reaction was initiated by hydride transfer and stopped-flow spectroscopy showed that the reaction proceeded $\textit{via}$ a short-lived intermediate. Since no structural information …
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Self-assembly and aggregation of glucagon-like peptide 1 and its analogues
… slightly slows down the fibrillation rate. Energy Landscape Theory was employed to investigate and rationalize the conformational behaviour and aggregation propensity of GLP-1 in different protonation states. Under all conditions studied, the GLP-1 energy landscape possesses a multi-funnel …