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Showing 1 to 15 of 15 for “"protein modeling"”.
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MARKOV STATE MODELS AND THEIR APPLICATIONS IN PROTEIN FOLDING SIMULATION, SMALL MOLECULE DESIGN, AND MEMBRANE PROTEIN MODELING
… on the application of Markov State Models on protein folding and designing of small drug-like molecules, as well as application of computational tools on the study of biological processes. The central focus of protein folding is to understand how proteins obtain their unique three-dimensional …
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Protein and Water Modeling in Computer-Aided Drug Discovery
… (CADD) is continuously evolving to improve protein modeling, a crucial step in the drug discovery process. However, limitations exist in how CADD accounts for the various configurations a protein can adopt due to different rotamer and protonation states of its residues. This thesis explores …
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De Novo Protein Structure Modeling from Cryoem Data Through a Dynamic Programming Algorithm in the Secondary Structure Topology Graph
<p>Proteins are the molecules carry out the vital functions and make more than the half of dry weight in every cell. Protein in nature folds into a unique and energetically favorable 3-Dimensional (3-D) structure which is critical and unique to its biological function. In contrast to other methods …
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A Geometric Approach for Deciphering Protein Structure from Cryo-EM Volumes
… creates new computational challenges for protein structure identification. In this dissertation, we present a suite of geometric algorithms to address several aspects of protein modeling using cryo-EM density maps. Specifically, we develop novel methods to capture the shape of density …
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Modeling proteins, making scientists : an ethnography of pedagogy and visual cultures in contemporary structural biology
… researchers who produce models and animations of protein molecules using three-dimensional interactive computer graphics. As they ramp up the pace of structure determination, modeling a vast array of proteins, these researchers are shifting life science research agendas from decoding genetic …
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Computational modeling of protein-protein and protein-peptide interactions
Protein-protein and protein-peptide interactions play a central role in various aspects of the structural and functional organization of the cell. While the most complete structural characterization is provided by X-ray crystallography, many biological interactions occur in complexes that will not …
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O antigen biosynthesis in Gram-negative bacteria: Characterization of alpha1,4-glucosyltransferase WclY from Escherichia coli O117 and development of glycosyltransferase inhibitors.
… the Glc-transferase to a GlcNAc-transferase. Protein modeling confirmed the role of Arg194 and other amino acids in the catalytic activity of WclY. Characterization of the enzyme has opened the door for testing of compounds with the potential to act as antimicrobial and antiseptic agents.
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Mutational analysis of the West Nile Virus NS4B protein
… 11kb in length encoding a single polyprotein that is cleaved by a combination of viral and host proteases to produce three structural and seven nonstructural proteins. The NS4B protein is a small hydrophobic protein approximately 27kD in size that is hypothesized to participate both in …
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Herbicide resistance in kochia and wheat: the loss and gain of weed control tools for wheat production
… is sufficient in causing dicamba resistance. Protein modeling suggests that while several amino acids are affected, a specific glycine-to-threonine substitution is likely the most important in causing resistance. Finally, the mutant allele of this gene segregates with reduced plant height and …
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Advances In Computer Aided Protein Structure Determination From Sparse Cryo Electron Microscopy Data
… data. Here we describe several tools for modeling with sparse experimental data, including a novel sampling strategy for de novo model completion and a novel refinement strategy for glycans with near atomic resolution cryoEM and x-ray crystallography data.
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Protein Design at Library Scale
Recent advances in de novo protein design have made it increasingly feasibleto create proteins with novel functions, driven by rapid progress in both com- putational modeling and high-throughput experimentation. Modern tools can explore vast sequence-structure spaces and evaluate biomolecular …
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Improving Structural Features Prediction in Protein Structure Modeling
<p>Proteins play a vital role in the biological activities of all living species. In nature, a protein folds into a specific and energetically favorable three-dimensional structure which is critical to its biological function. Hence, there has been a great effort by researchers in both …