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Search results for: HIV-1 INTEGRASE, INHIBITORS, DOCKING, ACTIVE SITE, ALLOSTERIC SITE,MOLECULAR DYNAMICS
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
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Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins
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Gluten-Free Bread with Cricket Powder—Mechanical Properties and Molecular Water Dynamics in Dough and Ready Product
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Editorial: smart modeling support for managing complexities and dynamics of knowledge-based systems-part 1
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Risk assessment of biocides in roof paint. Part 1
PublicationSzereg pokryć dachowych, jak farby dachowe, zawiera w swoim składzie biocydy. Dotychczas nie wiadomo do jakiego stopnia biocydy wymywane są z farb dachowych, a ponadto jakie ich stężenie może występować w systemach zbierających wodę deszczową. Zbadano podatność na wymywanie biocydów z różnych niemieckich farb dachowych oraz oszacowano ich stężenie w zebranej wodzie deszczowej
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Telomerase inhibition - unfulfilled hopes in the perfect molecular target
PublicationTelomerase plays a pivotal role in cell proliferation, homeostasis, and neoplastic transformation, making it a promising molecular target for cancer chemotherapy. Of note, although hTERT has been explored thoroughly as a target, none of the promising molecules has been approved as a drug until now. The subject of research conducted as part of my doctoral dissertation is explaining the cellular and molecular mechanism of action...
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DNA modification by 1-nitroacridine derivatives. Comparison of 32P-Postlabeling and restriction enzyme analysis method for the detection of DNA adducts formed by 1-nitroacridines C-1748 and C-857
Publication4-podstawione 1-nitroakrydyny reprezentują nową grupę pochodnych akrydyny, zsyntetyzowanych na Politechnice Gdańskiej. Metoda 32P-postlabellingu wykazała, że pochodne C-1748 i C-857 tworzą od 4-6 adduktów DNA w systemie komórkowym i bezkomórkowym o innym rozkładzie plam chromatograficznych, jednakże niezależnym od zastosowanego systemu aktywacyjnego. Metoda enzymatycznej analizy restrykcyjnej pozwoliła natomiast śledzić kinetykę...
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Functionalized Peptide Fibrils as a Scaffold for Active Substances in Wound Healing
PublicationTechnological developments in the field of biologically active peptide applications in medicine have increased the need for new methods for peptide delivery. The disadvantage of peptides as drugs is their low biological stability. Recently, great attention has been paid to self-assembling peptides that can form fibrils. Such a formulation makes bioactive peptides more resistant to enzymatic degradation and druggable. Peptide fibrils...
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Theoretical calculation of the physico-chemical properties of 1-butyl-4-methylpyridinium based ionic liquids
PublicationACCEPTED MAIonic liquids (ILs) have attracted much attention for their unique physicochemical properties, which can be designed as needed by altering the ion combinations. Besides experimental work, numerous computational studies have been concerned with prediction of physical properties of ILs. The results of molecular dynamics simulations of ILs depend strongly on the proper force field parameterization. Classical force fields...
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublicationShelterin is a six-protein complex (TRF1, TRF2, POT1, RAP1, TIN2, and TPP1) that also functions in smaller subsets in regulation and protection of human telomeres. Two closely related proteins, TRF1 and TRF2, make high-affinity contact directly with double-stranded telomeric DNA and serve as a molecular platform. Protein TIN2 binds to TRF1 and TRF2 dimer-forming domains, whereas Apollo makes interaction only with TRF2. To elucidate...
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Implementation of Molecular Dynamics and Its Extensions with the Coarse-Grained UNRES Force Field on Massively Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and Thermodynamics
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Nuclear quantum effects in a HIV/cancer inhibitor: The case of ellipticine
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Evaluating experimental molecular physics studies of radiation damage in DNA*
PublicationThe field of Atomic and Molecular Physics (AMP) is a mature field exploring the spectroscopy, excitation, ionisation of atoms and molecules in all three phases. Understanding of the spectroscopy and collisional dynamics of AMP has been fundamental to the development and application of quantum mechanics and is applied across a broad range of disparate disciplines including atmospheric sciences, astrochemistry, combustion and environmental...
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Independent dynamics of low, intermediate, and high frequency spectral intracranial EEG activities during human memory formation
PublicationA wide spectrum of brain rhythms are engaged throughout the human cortex in cognitive functions. How the rhythms of various frequency ranges are coordinated across the space of the human cortex and time of memory processing is inconclusive. They can either be coordinated together across the frequency spectrum at the same cortical site and time or induced independently in particular bands. We used a large dataset of human intracranial...
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Exploring the cost-effectiveness of high versus low perioperative fraction of inspired oxygen in the prevention of surgical site infections among abdominal surgery patients in three low- and middle-income countries
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EDD – Economic Benefit Analysis of Extending Dry Docking Interval
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Glucosylceramide Mimics: Highly Potent GCase Inhibitors and Selective Pharmacological Chaperones for Mutations Associated with Types 1 and 2 Gaucher Disease
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Branched pentapeptides as potent inhibitors of the vascular endothelial growth factor 165 binding to Neuropilin-1: Design, synthesis and biological activity
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Identification of X-DING-CD4, a new member of human DING protein family that is secreted by HIV-1 resistant CD4+ T cells and has anti-viral activity
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Lattice dynamics of Mg2SiO4
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Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins
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Self-assembly and interactions of short antimicrobial cationic lipopeptides with membrane lipids: ITC, FTIR and molecular dynamics studies
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MM/PBSA analysis of molecular dynamics simulations of bovine beta-lactoglobulin: free energy gradients in conformational transitions?
PublicationPraca dotyczy pH zależnych zmian konformacyjnych EF pętli beta-laktoglobuliny. Zmiany te są śledzone za pomocą metod obliczeniowych chemii (dynamika molekularna oraz metody MM/PBSA).
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Modelling of planar movement dynamics of upper limb
PublicationThe original model describing planar movement dynamics of upper limb is presented. The upper limb is modelled as two-joints system loaded by external forces and internal forces of striated skeletal muscles. A behaviour of each muscle is modelled as a system composed of serially linked rheologic fragments that have different mechanical properties. These muscle models allow us to simulate a behaviour of short fusiform muscle (3DOF...
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Research on Linear Actuators for Active Foil Bearings
PublicationActive foil bearings are a kind of gas foil bearing. They contain actuators which allow for modification of the bearing sleeve size and the shape of the lubrication gap. Rotor vibrations can be actively controlled by these changes. It is possible, among other things, to reduce the starting torque, control the vibration amplitude at different speeds and improve operational safety. Prototypes of active foil bearings are being developed...
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Molecular Design Using Selected Concentration Effects in Optically Activated Fluorescent Matrices
PublicationMolecular physics plays a pivotal role in various fields, including medicine, pharmaceuticals, and broader industrial applications. This study aims to enhance the methods for producing specific optically active materials with distinct spectroscopic properties at the molecular level, which are crucial for these sectors, while prioritizing human safety in both production and application. Forensic science, a significant socio-economic...
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Mapping the Transglycosylation Relevant Sites of Cold-Adapted β-D-Galactosidase from Arthrobacter sp. 32cB
PublicationB-Galactosidase from Arthrobacter sp. 32cB (ArthbetaDG) is a cold-adapted enzyme able to catalyze hydrolysis of beta-D-galactosides and transglycosylation reaction, where galactosyl moiety is being transferred onto an acceptor larger than a water molecule. Mutants of ArthbetaDG D207A and E517Q were designed to determine the significance of specific residues and to enable formation of complexes with lactulose and sucrose and to...
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Active Dynamic Thermography in Medical Diagnostics
PublicationThis is an overview of active thermal imaging methods in medical diagnostics using external thermal stimulation. In this chapter, several clinical cases diagnosed using the active dynamic thermography method, ADT, are presented. Features of this technology are discussed and main advantages underlined. Applications in skin burn diagnostics and quantitative evaluation leading to modern classification of burned patients for further...
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Novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(1,3,5-triazin-2-ylamino)guanidine derivatives: Inhibition of human carbonic anhydrase cytosolic isozymes I and II and the transmembrane tumor-associated isozymes IX and XII, anticancer activity, and molecular modeling studies
PublicationA series of novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(6-substituted-4-chloro-1,3,5-triazin-2-ylamino)guanidine derivatives 9–20 have been synthesized by substitution of chlorine atom at the 1,3,5-triazine ring in compounds 5–8 with 3- or 4-aminobenzenesulfonamide and 4-(aminomethyl)benzenesulfonamide hydrochloride. All the synthesized compounds were evaluated for their inhibitory activity toward hCA I, II,...
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Emerging anticancer activity of candidal glucoseamine-6-phosphate synthase inhibitors upon nanoparticle-mediated delivery
PublicationNumerous glutamine analogues have been reported as irreversible inhibitors of the glucosamine-6-phosphate (GlcN-6-P) synthase in pathogenic Candida albicans in the last 3.5 decades. Among the reported inhibitors, the most effective N3-(4-methoxyfumaroyl)-L-2,3- diaminopropanoic acid (FMDP) has been extensively studied in order to develop its more active analogues. Several peptide−FMDP conjugates were tested to deliver FMDP to its...
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Phosphate tricyclic coumarin analogs as steroid sulfatase inhibitors: synthesis and biological activity.
PublicationIn the present work, we report convenient methods for the synthesis and biological evaluation of phosphate tricyclic coumarin derivatives as potential steroid sulfatase inhibitors. The described synthesis includes the straightforward preparation of 7-hydroxy-2,3-dihydro-1H-cyclopenta[c]chromen-4-one, 3-hydroxy-7,8,9,10-tetrahydro-6H-benzo[c]chromen-6-one and 3-hydroxy-8,9,10,11-tetrahydro-7H-cyclohepta[c]chromen-6-one modified...
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The dynamics of the total output of the fishery sector: The case of Indonesia
PublicationThe purpose of this study is to analyze the dynamics of the total output of the Indonesian fishery industry when the changes of the final demand occur. This study employs a demand-pull Input-Output (IO) quantity model, one of the calculation tools in the IO analysis, as an analysis instrument. Two conditions are noticed in calculation and analysis parts, namely (1) “whole sector change”, and (2) “pure change”. An initial period...
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Investigation of the laser generated ablation plasma plume dynamics and plasma plume sound wave dynamics
PublicationWe investigated the dynamics of laser generated ablation plasma plume expanding in ambient air and dynamics of the sound wave generated by the expanding plasma. The ablation plasma plume was generated during nanosecond laser micromachining of the thin metal foil. The time-resolved images of the expanding plasma plume and sound wave were captured at several nanosecond intervals. Using captured images the expansion rate of the plasma...
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On dynamics of origami-inspired rod
PublicationWe discuss the dynamics of a relatively simple origami-inspired structure considering discrete and continuum models. The latter was derived as a certain limit of the discrete model. Here we analyze small in-plane deformations and related equations of infinitesimal motions. For both models, dispersion relations were derived and compared. The comparison of the dispersion relations showed that the continuum model can capture the behavior...
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Steroid Sulfatase Inhibitors Based on Phosphate and Thiophosphate Flavone Analogs
PublicationA series of phosphate and thiophosphate flavone derivatives were synthesized and biologically evaluated in vitro for inhibition of steroid sulfatase (STS) activity. The described synthesis includes the straightforward preparation of 7-hydroxy-2-phenyl-4H-chromen-4-one 3a, 2-(4-fluorophenyl)-7-hydroxy-4H-chromen-4-one 3b, 7-hydroxy-2-(4-(trifluoromethyl)phenyl)-4H-chromen-4-one 3c, 7-hydroxy-2-(p-tolyl)-4H-chromen-4-one 3d modified...
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Molecular Targets for Anticandidal Chemotherapy
PublicationA relatively small number of anticandidal chemotherapeutics used in clinical practice is at least in part consequence of a limited number of their molecular targets: ergosterol in the membrane, lanosterol demethylase, b(1!3) glucan synthase, and DNA/RNA biosynthesis. Much more potential novel targets have been revealed by the comparative genomic studies identifying essential genes unique for Candida albicans or resulted from recognition...
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Synthesis and biological evaluation of fluorinated 3-phenylcoumarin-7-O-sulfamate derivatives as steroid sulfatase inhibitors
PublicationIn the present work, we report the initial results of our study on a series of 3-phenylcoumarin sulfamate-based compounds containing C-F bonds as a novel inhibitors of steroid sulfatase (STS). The new compounds are potent STS inhibitors, possessing more than 10 times higher inhibitory potency than coumarin-7-O-sulfamate. In the course of our investigation, compounds 2b and 2c demonstrated the highest inhibitory effect in the enzymatic...
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Comparison of active proximity radars for the wearable devices
PublicationTwo methods of object position and movement estimation in relation to the user of smart glasses were investigated. An active infrared and ultrasonic methods of the obstacle detection were presented and compared. Application of these methods depend on active transducers type (physical medium used), geometry and surface properties of detected objects and their movement direction and speed. In the article properties of both detectors...
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Dynamics of algae growth and nutrients in experimental enclosures culturing bighead carp and common carp: Phosphorus dynamics
PublicationThis is the third paper of the series about “Dynamics of algae growth and nutrients in experimental enclosures culturing bighead carp and common carp”. In this paper, phosphorus dynamics were investigated under the condition of culturing bighead carp and common carp with added fish food (nitrogen dynamics is discussed in the second paper because their behaviors are so different from each other). Nearly fifty days’ observation results...
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Active Power Quality Controllers
PublicationDynamic Static Synchronous Compensator is the most important controller for distribution networks and probably in SEEN. It has been widely used since the 1990s to regulate system voltage precisely, improve voltage profile, reduce voltage harmonics, reduce transient voltage disturbances and load compensation. Rather than using conventional capacitors and inductors combined with fast switches, the D-STATCOM uses a power-electronics...
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Dynamics of Antimicrobial Peptide Encapsulation in Carbon Nanotubes: The Role of Hydroxylation
PublicationIntroduction: Carbon nanotubes (CNTs) have been widely employed as biomolecule carriers, but there is a need for further functionalization to broaden their therapeutic application in aqueous environments. A few reports have unraveled biomolecule–CNT interactions as a measure of response of the nanocarrier to drug-encapsulation dynamics. Methods: Herein, the dynamics of encapsulation of the antimicrobial peptide HA-FD-13 (accession...
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Effect of selected ammonia escape inhibitors on carbon dioxide capture and utilization via calcium carbonate precipitation
PublicationCarbon dioxide was used to precipitate CaCO3 with CaCl2 solution in the presence of NH3 as a CO2 absorption promoter. Compounds that were previously indicated as inhibitors of ammonia escape during CO2 absorption were also added to the reaction mixture. Inorganic salts, i.e. ZnCl2, CuCl2, CoCl2, and organic substances, i.e. glycerol, ethylene glycol and triethanolamine were tested inhibitors in this work. A model post-distillation...
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Measurements of Subnanometer Molecular Layers
PublicationSelected methods of formation and detection of nanometer and subnanometer molecular layers were shown. Additionally, a new method of detection and measurement with subnanometer resolution of layers adsorbed or bonded to the gate dielectric of the ion selective field effect transistor (ISFET) was presented.
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An Overview of Several Inhibitors for Alzheimer’s Disease: Characterization and Failure
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Determination of the active ingredient in pharmaceutical gel formulation by NIR spectroscopy
PublicationPharmaceuticals of their intended must be thoroughly controlled. The traditional analytical methods are very costly and time consuming. NIR spectroscopy allows to analyze pharmaceutical materials very quickly and with very low costs. First pharmaceutical applications of the NIR spectroscopy appeared with some incuriosity in the late 1960s. Application of NIR in the contemporary pharmaceutical industry is very large. The most common...
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Balancing energy consumption in limited power grid with active front-end and three phase dual active bridge system
PublicationPaper deals with simulation analysis of bidirectional power converters system for charging station of electric vehicle in condition of limited power source in city infrastructure. In case of incapability to provide additional power supply through the grid by virtue of historical, architectural and economic reasons it is possible to solve this issue by implementation of mobile battery-powered supply source. The proposed bidirectional...
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Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA
PublicationTelomeres are specialized nucleoprotein assemblies that protect the ends of linear chromosomes. In humans and many other species, telomeres consist of tandem TTAGGG repeats bound by a protein complex known as shelterin that remodels telomeric DNA into a protective loop structure and regulates telomere homeostasis. Shelterin recognizes telomeric repeats through its two major components known as Telomere Repeat-Binding Factors, TRF1...
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Neuroprotective Effect of SGLT2 Inhibitors
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Proteinase 3 phosphonic inhibitors
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X-ray Photoelectron Spectroscopy of Carboxylic Acids as Corrosion Inhibitors of Aluminium Alloys
PublicationThe datasets, titled X-ray Photoelectron Spectroscopy studies of citric acid adsorption on aluminium alloy 5754 in alkaline media and X-ray Photoelectron Spectroscopy studies of various carboxylic acids adsorption on aluminium alloys in alkaline media, contain XPS studies of the corrosion inhibitory action of selected dicarboxylic acids towards commercially available aluminium alloy 5754 in alkaline media at pH=11. These datasets...