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Showing 1 to 8 of 8 for “"de novo protein design"”.
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Generative Diffusion Models Towards De Novo Protein Design
De novo protein design aims to generate proteins with desired functions by rationally engineering novel protein structures and sequences. The structure requires modeling continuous 3D coordinates of atoms with rigid biochemical constraints of the polymer chain while the sequence is a series of …
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Uncovering Biophysical Determinants Of Oxidoreductase Function Through De Novo Protein Design
Oxidoreductases are a diverse class of enzymes defined by their chemical role of transferring electrons from one substrate to another. Comprising the functional cores of photosynthetic, chemosynthetic, and cellular respiratory machinery, “redox proteins” and the catalysis they enable form the …
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Toward a Database of Geometric Interrelationships of Protein Secondary Structure Elements for De Novo Protein Design, Prediction and Analysis
… methods of analyzing, simulating, and modeling proteins are essential towards understanding protein structure and its interactions. Computational methods are easier as not all protein structures can be determined experimentally due to the inherent difficultly of working with some …
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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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Mutagenic effects on protein folding and stability
… sequence information dictates the formation of protein structure is critical for accurate prediction of structure, for de novo protein design, and for understanding protein folding and misfolding. Based on extensive studies in peptide and protein systems, the pattern of polar and nonpolar amino …
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Supercharging: An Investigation into the Effects of External Amino Acid Residue Charge on the Solubility and Internal Electric Character of Bound Ligands in a Heme-Binding de novo-Designed Protein
<p>De novo protein design offers many interesting prospects both as a means to better understand natural protein dynamics and as a potential resource in biomedical and industrial applications. In this work I describe the modification of a simple, well-characterized heme-binding protein by altering …
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Network modularity and local environment similarity as descriptors of protein structure
As the number of solved protein structures increases, the opportunities for meta-analysis of this dataset increase too. Here we explore two approaches for analysing protein structure, both starting from the three-dimensional co-ordinates of each atom within the structure, which are then abstracted …
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Coordination Geometries in Metallobundles Enforcing Oxidative and Hydrolytic Catalysis and Designing Biomaterials for Use As Antimicrobials
<p>De novo protein design permits discovery of intricate folds and functions emulating natural enzymes in simpler, yet robust model constructs. Helical bundles serve as premier scaffolds to incorporate diverse reactivities from oxidative, reductive, to hydrolytic transformations observed in much …