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Showing 1 to 18 of 18 for “"Secondary structure elements"”.
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Toward a Database of Geometric Interrelationships of Protein Secondary Structure Elements for De Novo Protein Design, Prediction and Analysis
… 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 proteins. In order to predict, design, analyze, simulate or model a …
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A Geometric Approach for Deciphering Protein Structure from Cryo-EM Volumes
… with the state-of-the-art being 3.6A, where secondary structure elements can be visually identified but not individual amino acid residues. This lack of atomic level resolution creates new computational challenges for protein structure identification. In this dissertation, we present a suite …
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Projecte Borges plus
… conformation and geometrical relations among secondary structure elements. This system, with high performance and Big Data capabilities will be at the heart of software developed at the IBMB-CSIC to solve protein structures and will be operative on the local network and portable to …
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Deep Learning for Segmentation Of 3D Cryo-EM Images
… complexes. However, accurate detection of secondary structures is still challenging when cryo-EM density maps are at medium resolutions (5-10 Å). Most existing methods are image processing methods that do not fully utilize available images in the cryo-EM database. In this paper, we present …
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Computational Development for Secondary Structure Detection From Three-Dimensional Images of Cryo-Electron Microscopy
… from three-dimensional (3D) density images, secondary structure elements (SSEs) such as alpha-helices and beta-sheets can still be detected. The accuracy of SSE detection from the volumetric protein density images is critical for <em>ab initio</em> backbone structure derivation in cryo-EM. So …
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Biophysical Characterization of the vOTU Proteases from the CCHF and Dugbe Nairoviruses
… these substrate predilections, the X-ray crystal structures of the vOTUs from both CCHFV and DUGV were each solved covalently bound with Ub. These structures exposed unique secondary structure elements compared to other members of the OTU superfamily that offer understanding into why certain …
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Method Development And Applications To Screening And Characterization Of Rrna-Targeting Small Molecules
… results show that DHR23 has preferred binding to structured RNA as compared to ssRNA, as well as a modest preference for the A-site RNA. Also our results indicate that modified nucleotides at or near the ligand-binding pocket may affect binding affinity of small molecules.</p> <p>In summary, the …
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Investigation into the role of sequence-driven-features and amino acid indices for the prediction of structural classes of proteins
… to determine the function of a protein the structure must be known because the structure dictates its physical capabilities. A protein is generally classified into one of the four main structural classes, namely all-α, all-β, α + β or α / β, which are based on the arrangements and gross …
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An Alternative View of the Templates and Functions of RNA Polymerase II
… the left-hand tip region of the HDV rod-like structure, serves as a template for efficient transcription. The transcription reaction is highly sensitive to α-amanitin in HeLa cell NE, but it is partially resistant to this toxin in NE from PMG cells that contain an α-amanitin resistant allele …
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De Novo Protein Structure Modeling from Cryoem Data Through a Dynamic Programming Algorithm in the Secondary Structure Topology Graph
… and energetically favorable 3-Dimensional (3-D) structure which is critical and unique to its biological function. In contrast to other methods for protein structure determination, Electron Cryorricroscopy (CryoEM) is able to produce volumetric maps of proteins that are poorly soluble, large and …
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Language like behavior in protein secondary structure and analysis of mitochondrial genomes and transposable elements in Antarctic notothenioid fishes
… the Menzerath Altman Law (MA law) to examine the secondary structure of transcribed proteins. This law, derived within the field of linguistics, states that “the longer the system, the smaller its parts,” presenting an energy-balance principle in which system-level growth is compensated for by the …
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De Novo Protein Structure Modeling and Energy Function Design
<p>The two major challenges in protein structure prediction problems are (1) the lack of an accurate energy function and (2) the lack of an efficient search algorithm. A protein energy function accurately describing the interaction between residues is able to supervise the optimization of a protein …
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Atomistic simulation of self-organization in semiconducting polymers and polypeptides with molecular dynamics and Monte Carlo methodologies
In soft nanostructured materials based on chain molecules (typical examples include organic semiconducting polymers and polypeptides), chain self-organization at the nanoscale and mesoscale completely controls their macroscopic behavior and functionality. Although the equilibrium structure of many …
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Fantastic ribonucleoprotein complexes and how to study them. Architectural principles of regulatory assemblies in bacteria.
… triggers assembly of higher order complexes. The structures suggest that secondary structure elements and the sequence of the target RNA determine the quaternary structure of the Hfq-Crc translation-repression assembly, introducing a degree of structural diversity that is accommodated by …
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Analysis of Molecular Dynamics Simulations of Protein Folding
… a few trivial features like early formation of secondary structure, no commonalities between trajectories were found. There were no units of residues or atoms found moving in concert across the trajectories. A flipping transition, corresponding to the flipping of helix 1 relative to the plane …
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Using structure to explore the sequence alignment space of remote homologs
The success of protein structure modeling by homology requires an accurate sequence alignment between the query sequence and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence …
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STRUCTURAL AND FUNCTIONAL STUDIES OF F-BOX-ONLY PROTEIN FBXO7 AND ITS INTERACTIONS WITH PROTEASOME INHIBITOR PI31
… this dissertation are to elucidate the molecular structures underlying the functions of Fbxo7 and the interaction with its protein partners, such as proteasome inhibitor PI31. The best known biological function of Fbxo7 is its role as the substrate-recognition subunit of the SCFFbxo7 …
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Sample preparation of membrane proteins suitable for solid-state MAS NMR and development of assignment strategies
Although the basic structure of biological membranes is provided by the lipid bilayer, most of the specific functions are carried out by membrane proteins (MPs) such as channels, ion-pumps and receptors. Additionally, it is known, that mutations in MPs are directly or indirectly involved in many …