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Search results for: PROTEIN FOLDING
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Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
PublicationCritical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on...
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Rotational molding of polylactide (PLA) composites filled with copper slag as a waste filler from metallurgical industry
PublicationThe research work carried out so far indicates the ever wider possibilities and demand for shaping composite products in the rotational molding technology. This trend was the main reason to use waste-based filler from the metallurgical process as a filler for manufacturing polylactide (PLA)-based remolded composites. Copper slag (CS) was introduced in the single-step processing method to PLA matrix at 5, 10, 20, and 35 wt%. The...
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Adaptive resolution-constrained scalar multiple-description coding
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Formation of Protein Networks between Mucins: Molecular Dynamics Study Based on the Interaction Energy of the System
PublicationMolecular dynamics simulations have been performed for a model aqueous solution of mucin. As mucin is a central part of lubricin, a key component of synovial fluid, we investigate its ability to form cross-linked networks. Such network formation could be of major importance for the viscoelastic properties of the soft-matter system and crucial for understanding the lubrication mechanism in articular cartilage. Thus,the inter- and...
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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublicationIn this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the...
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Sulforaphane, a cruciferous vegetable-derived isothiocyanate, inhibits protein synthesis in human prostate cancer cells
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CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures
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Comparison of Antioxidant Activity of Protein Isolates Derived from Selected Dry-Cured Meat Products
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The Escherichia coli RNA polymerase alpha subunit and transcriptional activation by bacteriophage lambda CII protein.
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Mitogen activated protein kinase 4 (MPK4) influences growth in Populus tremula L.×tremuloides
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Rapeseed Meal Waste Biomass as Single-Cell Protein Substrate for Nutritionally-Enhanced Feed Component
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A cryptic ribosome binding site, false signals in reporter systems and avoidance of protein translation chaos
PublicationThe expression of reporter gene may be induced by activation of cryptic signalling sequences, as we found while constructing the mutS-lacZ fusion gene. We cloned the Escherichia coli lacZ gene encoding beta-galactosidase into a plasmid vector carrying the Thermus thermophilus mutS gene. The clones expected to produce beta-galactosidase as the C-terminal fusion were selected for the complementation of beta-galactosidase activity...
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E2/E3‐independent ubiquitin‐like protein conjugation by Urm1 is directly coupled to cysteine persulfidation
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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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Methodology of Selecting the Optimal Receptor to Create an Electrochemical Immunosensor for Equine Arteritis Virus Protein Detection
PublicationThe study reports a methodology of selecting the optimal receptor to create an electrochemical immunosensor for equine arteritis virus (EAV) protein detection. The detection was based on antigen recognition by antibodies immobilized on gold electrodes. Modification steps were controlled by electrochemical impedance spectroscopy and cyclic voltammetry measurements. In order to obtain the impedance immunosensor with the best parameters,...
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Post mortem changes in M. iliotibialis lateralis muscle protein profile of emu (Dromaius novaehollandiae)
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Excessive amount of lactose in the diet of two-week-old calves induces urinary protein changes
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublicationEmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the...
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Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA
PublicationAn essential feature of replication initiation proteins is their ability to bind to DNA. In this work, we describe a new domain that contributes to a replication initiator sequence-specific interaction with DNA. Applying biochemical assays and structure prediction methods coupled with DNA–protein crosslinking, mass spectrometry, and construction and analysis of mutant proteins, we identified that the replication initiator of the...
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Methodology of Selecting the Optimal Receptor to Create an Electrochemical Immunosensor for Equine Arteritis Virus Protein Detection
PublicationThe study reports a methodology of selecting the optimal receptor to create an electrochemical immunosensor for equine arteritis virus (EAV) protein detection. The detection was based on antigen recognition by antibodies immobilized on gold electrodes. Modification steps were controlled by electrochemical impedance spectroscopy and cyclic voltammetry measurements. In order to obtain the impedance immunosensor with the best parameters,...
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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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Study of the influence of thermal factors on the welding process of polyethylene gas pipelines,
PublicationA one-dimensional calculation scheme is proposed with the help of which it is possible to determine and set the technological parameters with the accuracy to be realized in production conditions: the temperature of the heating element and the heating time, which allows maximum mechanization of the technological operations of polyethylene gas pipelines welding. The numerical value of the coefficient of temperature for polyethylene...
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TIRE/ROAD NOISE AND TIRE ROLLING RESISTANCE ON PROTOTYPE PERS SURFACE
PublicationPoroelastic road surfaces are characterized by low noise of tires running on them.Road pavements of this type are promising solution to problems related to traffic noise in cities and on rural roads. Some technical problems still have to be solved, in particular regarding durability and skid resistance on wet surface. Ongoing and planned works are to contribute to create a quiet, durable and safe road surface, which will become...
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Degradation of the Concrete Railway Track Bed Located in the Vicinity of the Loading Wharf
PublicationThe following article describes the damages of the concrete railway track bed at the place of unloading petroleum products located in the immediate vicinity of the cargo berth. The concrete of the track bed has been a subject to degradation as a result of many years of exploitation resulting, inter alia, in its cyclical flooding of petroleum products during the unloading and loading of rail tankers. Repairs carried out in the previous...
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Guided wave propagation for assessment of adhesive bonding between steel and concrete
PublicationAdhesive bonding is becoming more increasingly important in joining of structural elements. In civil engineering, there is a growing interest in connection by adhesive bonding in steel-concrete flexural members. This study concerns the guided wave propagation technique applied to condition assessment of an adhesive connection between a steel member and a concrete beam. Various states of degradation were considered by producing...
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Bayesian Optimization for solving high-frequency passive component design problems
PublicationIn this paper, the performance of the Bayesian Optimization (BO) technique applied to various problems of microwave engineering is studied. Bayesian optimization is a novel, non-deterministic, global optimization scheme that uses machine learning to solve complex optimization problems. However, each new optimization scheme needs to be evaluated to find its best application niche, as there is no universal technique that suits all...
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The concept of a new two-stage fuse for high power pulse forming
PublicationThis manuscript introduces the concept, physical operating principle and studies on a new and unique two stage forming fuse (TSFF) with interstage spark gap commutation and presents its application for forming high power pulses of extreme parameters. The paper classifies TSFF performance and compares it with conventional single-stage forming fuses. The conclusions are supported by analytical and experimental studies in laboratory...
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The Method of Finding the Optimal Spindle Speed When Milling Flexible Details
PublicationThe paper presents a new method of vibration reduction during milling of flexible details. The method consists in selecting the optimal spindle speed, based on the natural frequency of the workpiece. For this purpose, an original method was created, which is based on minimizing the work of cutting forces in the direction of the depth of cutting. The effectiveness of the method has been proved by comparing the RMS values of vibration...
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Nanotubular Titanium Oxide Layers for Enhancement of Bone-Implant Bonding and Bioactivity
PublicationThe present paper describes the techniques to improve the bioactivity of titanium and enhance the bone-implant bonding ability by the electrochemical anodization to fabricate titania nanotube arrays (TiO2).
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Two tests for adhesive bonding long term characterization: principles and applications
PublicationThis article describes recent refinement of the traditional wedge test technique used to characterize durability of the adhesive joints. We propose two types of measuring protocols to monitor precisely and continuously the propagation of an "effective" crack during long term mode I fracture mechanic test. First method is directly derived from the traditional wedge test technique and consist in monitoring the surface strain of adherent...
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Impact of intense rains and flooding on mercury riverine input to the coastal zone
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The effect of disturbance caused by rivers flooding on ground beetles (Coleoptera: Carabidae)
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Use of Neural Networks in Diagnostics of Rolling-Element Bearing of the Induction Motor
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Modeling of Heat Source Based on Parameters of Electron Beam Welding Process
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Numerical Simulation of Electron Beam Welding Process of Inconel 706 Sheets
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Finding Temperature Distribution at Heat Recovery Unit Using Genetic Algorithms
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Analysis of the amount of retained austenite in the structure of steel rolls for sheet rolling
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Solving Multi-Ship Encounter Situations by Evolutionary Sets of Cooperating Trajectories
PublicationAutor zaproponował nowe podejście do sytuacji kolizyjnych na morzu. Polega ono na zastąpieniu ewolucyjnej trajektorii własnej ewolucyjnym zbiorem trajektorii wszystkich obiektów. Podejście to umożliwia predykcję manewrowania obiektów obcych przy jednoczesnym zachowaniu efektywności algorytmów ewolucyjnych. Dodatkowo, opracowany już wstępnie przez autorów zbiór kryteriów, ograniczeń i operatorów specjalizowanych powinien zapewnić...
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An approximative scheme of finding almost homoclinic solutions for a class of Newtonian systems
PublicationW niniejszej pracy badamy istnienie rozwiązań prawie homoklinicznych (ang. almost homoclinic solutions) dla pewnej klasy układów Newtona. Rozwiązanie prawie homokliniczne otrzymujemy jako granicę ciągu rozwiązań okresowych dla pewnego ciągu równań różniczkowych.
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Nanotubular Ti Oxide Layers for Enhancement of Bone-Implant Bonding and Bioactivity
PublicationAbstrakt artykułu pt. ''Nanotubular Ti Oxide Layers for Enhancement of Bone-Implant Bonding and Bioactivity''. The paper describes techniques to improve the bioactivity of titanium and ehnahnce the bone-implant bonding ability by the electrochemical anodization to fabricate titania nanotubular oxide layer.
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Representation of a built-up area in the numerical simulation of urban flash flooding
PublicationPrzedstawiono wyniki modelowania powodzi miejskiej przy pomocy dwuwymiarowych równań de Saint-Venanta. Równania rozwiązano metodą objętości skończonych. Zaprezentowano dwie techniki reprezentacji obszarów zabudowanych w numerycznej symulacji powodzi - bezpośrednie wykluczenie budynków z siatki numerycznej oraz zastąpienie grup budynków terenami o znacznie zwiększonej szortkości powierzchni. W celu oceny wykorzystanych metod wykonano...
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Effect of welding conditions on susceptibility to cold cracking of underwater welded joints
PublicationPrzedstawiono wybrane aspekty spawalności stali przy spawaniu pod wodą metodą lokalnej komory suchej. Zwrócono szczególną uwagę na skłonność do tworzenia peknięć zimnych w SWC. Przy pomocy planowania doświadczeń określono ilościowy wpływ parametrów spawania na naprężenia krytyczne z próby implant.
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Interlayer defect evolution in an coating system on steel under hydromechanical loading
PublicationZaprezentowano wyniki pomiarów impedancyjnych obszaru międzywarstwowego w systemie powłokowym poddanym naprężeniom. Przedstawiono nowy sensor który jest zdolny do detekcji defektów w obszarze międzywarstwowym. Dwuwarstwowy system powłokowy przeznacziony do zastosowań morskich zbadano w celu określenia jego odporności na oddziaływanie cyklicznych naprężeń i zanurzeń w 3% roztworze NaCl.
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An Approximate Linear Analysis of Structures Utilizing Incremental Loading of Force Method
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Influence of the substrate loading on the quality and diameter distribution of SWCNT in alcohol‐CVD
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The Use of NaOH Solutions for Fouling Control in a Membrane Bioreactor: A Feasibility Study
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Bonding interactions in oxydiacetate and thiodiacetate cobalt(II) and nickel(II) complexes
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POPULATION-BASED MULTI-AGENT APPROACH TO SOLVING MACHINE LEARNING PROBLEMS
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Computational issues of solving the 1D steady gradually varied flow equation
PublicationIn this paper a problem of multiple solutions of steady gradually varied flow equation in the form of the ordinary differential energy equation is discussed from the viewpoint of its numerical solution. Using the Lipschitz theorem dealing with the uniqueness of solution of an initial value problem for the ordinary differential equation it was shown that the steady gradually varied flow equation can have more than one solution....