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Showing 1 to 7 of 7 for “"flexible fitting"”.
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Structural analyses of the ribosome by hybrid approach
… hybrid approach, namely the molecular dynamics flexible fitting (MDFF) method, and apply it to the ribosome. We improved MDFF in two regards, first by incorporating structural symmetry information into the fitting protocol and second by the use of a so-called implicit solvent model. In pursuit …
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Computational study of the structure and function of membrane transport proteins
… MD simulations particularly Molecular Dynamics Flexible Fitting (MDFF) in its resolution exchange flavor ReMDFF, I present the results of the 2015-2016 Cryo-EM Model challenge. In this challenge that I participated, we employed the aforementioned methodologies to forward the field of structure …
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Investigating the mechanisms of protein synthesis using multi-resolution structural data
… level, we developed the molecular dynamics flexible fitting (MDFF) method that combines X-ray and cryo-EM data, furnishing atomic models of the ribosome corresponding to functional intermediates. The MDFF-derived atomic models, combined with molecular dynamics simulations and other …
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Methods for increasing model accuracy and simulation time scales of biological processes with molecular dynamics
… of these projects, where the molecular dynamics flexible fitting method for refining molecular structures of macromolecules using experimental electron density data is extended to be able to handle high-resolution density data, which are becoming increasingly commonplace. The third chapter …
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Multiscale Modeling of Biomolecular Complexes
… features present in the EM map to be used in the fitting process, while the model remains fully flexible and stereochemically correct. Validation for the molecular dynamics flexible fitting (MDFF) method using available crystal structures of protein and RNA in different conformations are …
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Investigating translational control of the ribosome using molecular dynamics simulations
The ribosome is one of the most basic cellular machines and is ubiquitous in all living cells, responsible for the translation of genes into functional proteins. The central task of the ribosome is to promote peptide-bond transfer reaction by precisely aligning substrates of protein synthesis in …
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Molecular modeling and simulation of bacterial chemosensory arrays
… dynamics (MD) simulation and Molecular Dynamics Flexible Fitting (MDFF). In addition, two of the primary techniques used to analyze the MD simulations presented in this dissertation are sketched out, namely structural clustering based on root- mean-square displacement (RMSD) and Principal …