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Showing 1 to 20 of 142 for “"protein structures"”.
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A series of advanced scoring functions in ranking protein structures
… functions or scoring functions can help rank protein structures models, guide the search and identify possible solutions. This is very important for protein structure prediction. A lot of work have been done in this area but none of them has achieved the desired result. It is therefore …
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Simulating, refining and modeling protein structures with multi-scale methods
… methods for refining, modeling and simulating protein structures in multi-scale resolution. Combining with experimental information from different structural biological method such as Fiber Diffraction, cryo-Electron Microscopy (cryo-EM), Small Angle X-ray Scattering (SAXS) and X-ray …
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Machine Learning for Reconstructing Dynamic Protein Structures from Cryo-EM Images
Proteins and other biomolecules form dynamic macromolecular machines that carry out essential biological processes responsible for life. However, studying the mechanisms of these biomolecular complexes at relevant atomic-scale resolutions is an extraordinarily challenging task in structural …
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Tunable Microchips for Imaging Protein Structures formed in Breast Cancer Cells
The breast cancer susceptibility protein, BRCA1, is a tumor suppressor that helps maintain genomic integrity. Changes in BRCA1 that effect DNA repair processes can fuel cancer induction. The Kelly lab, at the Virginia Tech Carilion Research Institute, has recently developed a new methodology that …
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Topology and geometry-based methods for quantifying the complexity of protein structures
… systems of filaments, such as those formed by proteins. In this dissertation we employ tools from knot theory in combination with available experimental data and molecular simulations to analyze the topological complexity of tau proteins. These proteins are involved in a class of …
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ChaperoNet: Distillation of Language Model Semantics to Folded Three-Dimensional Protein Structures
Determining the structure of proteins has been a long-standing goal in biology. Lan- guage models have been recently deployed to capture the evolutionary semantics of protein sequences, and as an emergent property, were found to be structural learn- ers. Enriched with multiple sequence alignments …
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In silico protein evolution by intelligent design: creating new and improved protein structures
Natural proteins perform a startling diversity of biological functions, but comprise a miniscule fraction of the theoretical sequence-structure space that polypeptides might occupy. The goal of protein design is to identify new free-energy minima in this sequence-structure landscape so as to expand …
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Formulation, physicochemical and rehydration properties of whey protein powders containing nanoparticulated whey protein structures
Whey proteins have important nutritional and functional properties, and are available commercially in multiple formats, ranging from protein concentrates to isolates. Diversification and enhancement of the functional properties of whey proteins is an ongoing area of research, which is driven by …
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The protein structures underlying receptor binding and membrane fusion of ecotropic murine leukemia viruses
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 1997.
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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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Calculating the structure-based phylogenetic relationship of distantly related homologous proteins utilizing maximum likelihood structural alignment combinatorics and a novel structural molecular clock hypothesis
… relationships and homology of species, proteins, or genes. Homology modeling, ligand binding, and pharmaceutical testing all depend upon the homology ascertained by dendrograms. Regardless of the specific algorithm, all dendrograms that ascertain protein evolutionary homology are …
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Prediction of Protein Function Using Statistically Significant Sub-Structure Discovery
Proteins perform a vast number of functional roles. The number of protein structures available for analysis continues to grow and, with the development of methods to predict protein structure directly from genetic sequence without imaging technology, the number of structures with unknown function …
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The Application of Pulsed Electron Paramagnetic Resonance to the Investigation of Protein Structure
… rare occasions orientations within biomolecular structures. Site directed spin labelling (SDSL) has provided a method for introducing EPR active species into protein structures, the majority of these species are too flexible for the use of orientation measurements unless their introduced into …
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Projecte Borges plus
… of software developed at the IBMB-CSIC to solve protein structures and will be operative on the local network and portable to supercomputing facilities such as the Gordon supercomputer in San Diego (SDSC).
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Improved Constrained Global Optimization for Estimating Molecular Structure From Atomic Distances
… (VDW) constraints to provide better quality protein structures. However, the improvement in more detailed structural features such as shape and chirality requires the integration of additional constraint types.</p> <p>This dissertation builds on the GNOMAD algorithm in using structural data …
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Investigating the evolution and functionality of closely related Wnt ligands in Drosophila melanogaster
… Wnt ligands were compared to each other and protein structures for each of the seven Wnt ligands in Drosophila were predicted to identify any similarities and differences in the protein structures. Protein structures were modelled using templates from the existing crystallised protein of …
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Highly Accurate Fragment Library for Protein Fold Recognition
<p>Proteins play a crucial role in living organisms as they perform many vital tasks in every living cell. Knowledge of protein folding has a deep impact on understanding the heterogeneity and molecular functions of proteins. Such information leads to crucial advances in drug design and disease …
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New Methods to Improve Protein Structure Modeling
<p>Proteins are considered the central compound necessary for life, as they play a crucial role in governing several life processes by performing the most essential biological and chemical functions in every living cell. Understanding protein structures and functions will lead to a significant …
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Towards a Prime Factorization of Proteins
… the case in the richly complex field of protein analysis, whereby unique and novel insights into the structural organization of proteins can help illuminate their functional space, and in particular lead toward a factorization of the structural space into a set of motif building blocks, …
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