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Search results for: PROTEIN EMBEDDING
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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublicationA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...
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PROTEIN EXPRESSION AND PURIFICATION
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Towards semantic-rich word embeddings
PublicationIn recent years, word embeddings have been shown to improve the performance in NLP tasks such as syntactic parsing or sentiment analysis. While useful, they are problematic in representing ambiguous words with multiple meanings, since they keep a single representation for each word in the vocabulary. Constructing separate embeddings for meanings of ambiguous words could be useful for solving the Word Sense Disambiguation (WSD)...
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Function and Frustration of Multi-Drug ABC Exporter Protein and Design of Model Proteins for Drug Delivery Using Protein Hydration Thermodynamics
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Elastic-contractile model proteins: Physical chemistry, protein function and drug design and delivery
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Protein & Cell
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PROTEIN JOURNAL
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Graph Vertex Embeddings: Distance, Regularization and Community Detection
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublicationTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...
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Dirichlet-to-Neumann and Neumann-to-Dirichlet embedding methods for bound states of the Dirac equation
PublicationZaprezentowano uogólnienie formalizmu operatorów Dirichleta-Neumanna (DtN) i Neumanna-Dirichleta (NtD) na przypadek równania Diraca. Przedstawiono zastosowanie tego formalizmu do znajdowania poziomów energetycznych cząstki Diraca związanej w potencjale.
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Dirichlet-to-Neumann and Neumann-to-Dirichlet embedding methods for bound states of the Schrodinger equation.
PublicationPrzeformułowano metodę Inglesfielda, stosowaną do obliczania własności stanów związanych równania Schrodingera, stosując formalizm operatorów całkowych Dirichleta-do-Neumanna(DtN) i Neumanna-do-Dirichleta (NtD). Wykorzystano zasady wariacyjne dla energii dopuszczające użycie funkcji próbnych nieciągłych wraz z pochodnymi. Podano metodę konstrukcji jąder operatorów DtN i NtD za pomocą rozwiązań zagadnienia własnego typu Steklova....
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Extension of the Unres Package for Physics-Based Coarse-Grained Simulations of Proteins and Protein Complexes to Very Large Systems
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Open-Set Speaker Identification Using Closed-Set Pretrained Embeddings
PublicationThe paper proposes an approach for extending deep neural networks-based solutions to closed-set speaker identification toward the open-set problem. The idea is built on the characteristics of deep neural networks trained for the classification tasks, where there is a layer consisting of a set of deep features extracted from the analyzed inputs. By extracting this vector and performing anomaly detection against the set of known...
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PROTEIN SCIENCE
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ADVANCES IN PROTEIN CHEMISTRY
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JOURNAL OF PROTEIN CHEMISTRY
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PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
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UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations
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Tissue fixed with formalin and processed without paraffin embedding is suitable for imaging of both peptides and lipids by MALDI-IMS
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PROTEUS
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Probiotics and Antimicrobial Proteins
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The Protein Folding Problem
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PROTEIN AND PEPTIDE LETTERS
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Embodying Intelligence in Autonomous Systems with the Use of Cognitive Psychology and Motivation Theories
PublicationThe article discusses, on a certain level of abstraction and generalization, a coherent anthropological approach to the issue of controlling autonomous robots or agents. A contemporary idea can be based on appropriate modeling of the human mind using the available psychological knowledge. One of the main reasons for developing such projects is the lack of available and effective top-down approaches resulting from the known research...
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Influence of Osmolytes on Protein and Water Structure: A Step To Understanding the Mechanism of Protein Stabilization
PublicationResults concerning the thermostability of hen egg white lysozyme in aqueous solutions with stabilizing osmolytes, trimethylamine-N-oxide (TMAO), glycine (Gly), and its N-methyl derivatives, N-methylglycine (NMG), N,N-dimethylglycine (DMG), and N,N,N-trimethylglycine (betaine, TMG), have been presented. The combination of spectroscopic (IR) and calorimetric (DSC) data allowed us to establish a link between osmolytes’ influence on...
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CURRENT PROTEIN & PEPTIDE SCIENCE
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Current Protocols in Protein Science
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Proteins
PublicationStruktura białek wpływa na ich wartość odżywczą, właściwości funkcjonalne wżywności oraz reakcje w surowcach i produktach żywnościowych. Warunki prze-chowywania oraz obróbki w przemyśle i w czasie przygotowywania kulinarnegowywołują przemiany białek istotne dla jakości żywności. Przez celowe, enzy-matyczne i chemiczne modyfikowanie składu i struktury białek można wpływaćna ich właściwości funkcjonalne w żywności i wartość...
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Embodying Intelligence in Autonomous and Robotic Systems with the Use of Cognitive Psychology and Motivation Theories
PublicationThe article discusses, on a certain level of abstraction and generalization, a coherent anthropological approach to the issue of controlling autonomous robots or agents. A contemporary idea can be based on appropriate modeling of the human mind using the available psychological knowledge. One of the main reasons for developing such projects is the lack of available and effective top-down approaches resulting from the known research...
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Alternative and New Protein Sources
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Stabilizing agents and protein stability
PublicationBiałka są kluczowymi elementami żywych organizmów, jak również efektywnymi katalizatorami w biotechnologii i medycynie. Szybki rozwój wielu gałęzi biotechnologii wiąże się z coraz większym zapotrzebowaniem na produkty białkowe charakteryzujące się wysoką stabilnością. Jednym ze sposobów osiągnięcia większej stabilności białek jest wykorzystanie małych związków organicznych, tzw. osmolitów. Do tej grupy związków należą aminokwasy,...
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Colloidal aspects of protein digestion
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On the Origin of Protein Superfamilies and Superfolds
PublicationDistributions of protein families and folds in genomes are highly skewed, having a small number of prevalent superfamiles/superfolds and a large number of families/folds of a small size. Why are the distributions of protein families and folds skewed? Why are there only a limited number of protein families? Here, we employ an information theoretic approach to investigate the protein sequence-structure relationship that leads to...
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Endocrine responses following exhaustive strength exercise with and without the use of protein and protein-carbohydrate supplements
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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
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Post-critical buckling of truncated conical carbon nanotubes considering surface effects embedding in a nonlinear Winkler substrate using the Rayleigh-Ritz method
PublicationThis research predicts theoretically post-critical axial buckling behavior of truncated conical carbon nanotubes (CCNTs) with several boundary conditions by assuming a nonlinear Winkler matrix. The post-buckling of CCNTs has been studied based on the Euler-Bernoulli beam model, Hamilton’s principle, Lagrangian strains, and nonlocal strain gradient theory. Both stiffness-hardening and stiffness-softening properties of the nanostructure...
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Occlusion phenomenon of redox probe by protein as a way of voltammetric detection of non-electroactive C-reactive protein
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PROTEIN ENGINEERING DESIGN & SELECTION
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t-SNE Highlights Phylogenetic and Temporal Patterns of SARS-CoV-2 Spike and Nucleocapsid Protein Evolution
PublicationWe propose applying t-distributed stochastic neighbor embedding to protein sequences of SARS-CoV-2 to construct, visualize and study the evolutionary space of the coronavirus. The basic idea is to explore the COVID-19 evolution space by using modern manifold learning techniques applied to evolutionary distances between variants. Evolutionary distances have been calculated based on the structures of the nucleocapsid and spike proteins.
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World Research Journal of Peptide and Protein
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Advances in Protein Chemistry and Structural Biology
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Current Topics in Peptide and Protein Research
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International Journal of Peptide and Protein Research
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AMYLOID-JOURNAL OF PROTEIN FOLDING DISORDERS
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Iron–Sulfur Cluster Biogenesis Chaperones: Evidence for Emergence of Mutational Robustness of a Highly Specific Protein–Protein Interaction
PublicationBiogenesis of iron–sulfur clusters (FeS) is a highly conserved process involving Hsp70 and J-protein chaperones. However, Hsp70 specialization differs among species. In most eukaryotes, including Schizosaccharomyces pombe, FeS biogenesis involves interaction between the J-protein Jac1 and the multifunctional Hsp70 Ssc1. But, in Saccharomyces cerevisiae and closely related species, Jac1 interacts with the specialized Hsp70 Ssq1,...
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The Role of Proteins in Food
PublicationThis chapter describes the effect of proteins on the sensory attributes and the biological value and safety of foods. The role of proteins depends on their amino acid composition and structure, on changes due to storage and processing, as well as on interactions with other food components. The effect on the sensory quality of foods is brought about by hydrophobicity, solubility, water holding capacity, gelling, film formation,...
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Apple pectin complexes with whey protein isolate
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Polysaccharide–Protein Complexes in a Coarse-Grained Model
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The investigation of the effects of counterions in protein dynamics simulations
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