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Search results for: CASP, COVID, EMA, MODEL ACCURACY, PROTEIN STRUCTURE PREDICTION, SARS-COV-2
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Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds
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Mining Knowledge of Respiratory Rate Quantification and Abnormal Pattern Prediction
PublicationThe described application of granular computing is motivated because cardiovascular disease (CVD) remains a major killer globally. There is increasing evidence that abnormal respiratory patterns might contribute to the development and progression of CVD. Consequently, a method that would support a physician in respiratory pattern evaluation should be developed. Group decision-making, tri-way reasoning, and rough set–based analysis...
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Remote learning among students with and without reading difficulties during the initial stages of the COVID-19 pandemic
PublicationThis article presents the results of a survey on yet under-researched aspects of remote learning and learning difficulties in higher education during the initial stage (March – June 2020) of the COVID-19 pandemic. A total of 2182 students from University of Warsaw in Poland completed a two-part questionnaire regarding academic achievements in the academic year 2019/2020, living conditions and stress related to learning and pandemic,...
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Influence of ESPAR Antenna Radiation Patterns Shape on PPCC-Based DoA Estimation Accuracy
PublicationIn the article, we show the influence of three different electronically steerable parasitic array radiator (ESPAR) antenna radiation patterns on the overall direction of arrival (DoA) estimation accuracy when power-pattern cross-correlation (PPCC) algorithm, relying on received signal strength (RSS) values, is used for the estimation. The ESPAR antenna designs were obtained for three optimization...
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<i>catena</i>-Poly[[[bis(thiourea-κS)cadmium]-di-μ-thiocyanato-κ<sup>2</sup>N:S;κ<sup>2</sup>S:N] dihydrate]
PublicationTytułowy związek tworzy jednowymiarowy łańcuch na skutek występowania mostkujących grup SCN pomiędzy atomami kadmu. Atomy kadmu obsadzają krystalograficzne środki symetrii i są koordynowane oktaedrycznie (zdeformowany oktaedr) przez 2 atomy S i 2 atomy N z mostkujących ligandow SCN oraz przez 2 atomy S z dwóch cząsteczek tiomocznika. Upakowanie jest wspomagane przez dodatkowe wiązania międzycząsteczkowe OH...S, NH...O i NH...N....
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Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology
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2-outer-independent domination in graphs
PublicationWe initiate the study of 2-outer-independent domination in graphs. A 2-outer-independent dominating set of a graph G is a set D of vertices of G such that every vertex of V(G)\D has at least two neighbors in D, and the set V(G)\D is independent. The 2-outer-independent domination number of a graph G is the minimum cardinality of a 2-outer-independent dominating set of G. We show that if a graph has minimum degree at least two,...
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The Major Heat Shock Proteins, Hsp70 and Hsp90, in 2-Methoxyestradiol-Mediated Osteosarcoma Cell Death Model
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Accuracy analysis of a mobile station location in the cellular networks
PublicationJakość usług lokalizacyjnych oferowanych w sieciach komórkowych zależy od efektywności estymacji położenia terminala ruchomego. Dokładność obecnie stosowanych metod lokalizacyjnych jest niewystarczająca, szczególnie w odniesieniu do wywołań w niebezpieczeństwie. Modyfikacja istniejących algorytmów może istotnie wpłynąć na zwiększenie dokładności lokalizowania terminala ruchomego przy jednocześnie niewielkich nakładach finansowych....
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Integration of protein tethering in a rapid and label-free SERS screening platform for drugs of abuse
PublicationSurface enhanced Raman spectroscopy (SERS) has emerged as a promising technique for the rapid and ultrasensitive detection of molecular species such as drugs of abuse in biofluids. Yet, it remains a significant challenge to create a viable screening tool for multiple drug classes, owing to the lack of affinity of certain species for the SERS substrate and to the matrix interference in complex media. Here we report a protein tethering...
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The Unfolded Protein Response: A Double-Edged Sword for Brain Health
PublicationEfficient brain function requires as much as 20% of the total oxygen intake to support normal neuronal cell function. This level of oxygen usage, however, leads to the generation of free radicals, and thus can lead to oxidative stress and potentially to age-related cognitive decay and even neurodegenerative diseases. The regulation of this system requires a complex monitoring network to maintain proper oxygen homeostasis. Furthermore,...
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Underground Water Level Prediction in Remote Sensing Images Using Improved Hydro Index Value with Ensemble Classifier
PublicationThe economic sustainability of aquifers across the world relies on accurate and rapid estimates of groundwater storage changes, but this becomes difficult due to the absence of insitu groundwater surveys in most areas. By closing the water balance, hydrologic remote sensing measures offer a possible method for quantifying changes in groundwater storage. However, it is uncertain to what extent remote sensing data can provide an...
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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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Experimental guinea pig model of dermatophytosis: a simple and useful tool for the evaluation of new diagnostics and antifungals
PublicationCelem badań było opracowanie prostego modelu zwierzęcego (świnki morskie) odpowiedniego do sprawdzania systemów diagnostycznych oraz terapii infekcji dermatofitów. Następujące zmienne były analizowane: przygotowanie skóry przez golenie versus użycie taśmy, testowy szczep Microsporum canis czy Trichophyton mentagrophytes jako czynnik etiologiczny, sposób inokulacji. Przebieg infekcji był oceniany poprzez ocenę zaczerwienienia i...
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The behavioural model of graphene field-effect transistor
PublicationThe behavioural model of a graphene field-effect transistor (GFET) is proposed. In this approach the GFET element is treated as a “black box” with only external terminals available and without considering the physical phenomena directly. The presented circuit model was constructed to reflect steady-states characteristics taking also into account GFET capacitances. The authors’ model is defined by a relatively small number of equations...
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A novel luminescent chemical sensor for the determination of Pb 2+ and Cu 2+ ions
PublicationSilica xerogel surface grafted with aminopropyl (PrNH2) groups was additionally treated by cetyltrimethylammonium bromide (CTAB) surfactant and ascorbic acid (asc) in alkaline solution. This material symbolized as SiO2-PrNH2-CTAB/asc, proved to be a stable luminescent material, exhibited an emission band peaked at 393 nm under excitation wavelength 335 nm. Time evolution of the band intensity suggests changes of defect concentration...
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Improving the accuracy of subgridding scheme in finite differences method based on Legendre polynomials expansion
PublicationIn this article the Legendre polynomials have been used to interpolate the field at the boundary of the meshes of different densities. The numerical verification of the proposed technique has been carried out in frequency domain. It has been shown that the accuracy of the presented method is very high and stable - the error monotonically decreases as a function of the refinement factor.
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2-Methoxyestradiol and Hydrogen Peroxide as Promising Biomarkers in Parkinson’s Disease
PublicationEstrogens function in numerous physiological processes including controlling brain cell growth and differentiation. 2-Meth- oxestradiol (2-ME2), a 17β-estradiol (E2) metabolite, is known for its anticancer effects as observed both in vivo and in vitro. 2-ME2 affects all actively dividing cells, including neurons. The study aimed to determine whether 2-ME2 is a potentially cancer-protective or rather neurodegenerative agent in a...
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Novel 2-alkythio-4-chloro-N-[imino(heteroaryl)methyl]benzenesulfonamide Derivatives: Synthesis, Molecular Structure, Anticancer Activity and Metabolic Stability
PublicationA series of novel 2-alkythio-4-chloro-N-[imino-(heteroaryl)methyl]benzenesulfonamide derivatives, 8–24, were synthesized in the reaction of the N-(benzenesulfonyl)cyanamide potassium salts 1–7 with the appropriate mercaptoheterocycles. All the synthesized compounds were evaluated for their anticancer activity in HeLa, HCT-116 and MCF-7 cell lines. The most promising compounds, 11–13, molecular hybrids containing benzenesulfonamide...
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The Use of Cluster Analysis to Evaluate the Impact of COVID-19 Pandemic on Daily Water Demand Patterns
PublicationProper determination of unitary water demand and diurnal distribution of water consumption (water consumption histogram) provides the basis for designing, dimensioning, and all analyses of water supply networks. It is important in the case of mathematical modelling of flows in the water supply network, particularly during the determination of nodal water demands in the context of Extended Period Simulation (EPS). Considering the...
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Crystal structure and physical properties of a novel ternary compound La15MoxGe9
PublicationWe present the synthesis, structural characterization and physical properties measurements of a new compound, La15MoxGe9 in Mn5Si3-type derived structure with interstitial Mo. The sample was synthesized by arc-melting method. La15MoxGe9 crystallizes in non-centrosymmetric hexagonal structure P63mc (#186) with lattice parameters a = b = 15.495(5) Å and c = 6.917(2) Å. The refinement on single X-ray diffraction data show that interstitial...
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Non-isolating 2-bondage in graphs
PublicationA 2-dominating set of a graph G=(V,E) is a set D of vertices of G such that every vertex of V(G)D has at least two neighbors in D. The 2-domination number of a graph G, denoted by gamma_2(G), is the minimum cardinality of a 2-dominating set of G. The non-isolating 2-bondage number of G, denoted by b_2'(G), is the minimum cardinality among all sets of edges E' subseteq E such that delta(G-E') >= 1 and gamma_2(G-E') > gamma_2(G)....
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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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Alternative and New Protein Sources
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Age, frequency of volunteering, and Present-Hedonistic time perspective predict donating items to people in need, but not money to combat COVID-19 during lock-down
PublicationRestrictions due to COVID-19 necessitated staying at home, but in some cases, encouraged charitable behavior, e.g., donating items to people in need (e.g., clothes, food), or money to support combatting COVID-19. Drawing on the previous findings regarding helping during disastrous situations and roles of time perspective in helping behaviors, the study tested the predictive value of age, gender, previous volunteering, altruistic...
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The hydration properties of protein stabilizer, trimethylamine-N-oxide in aqueous solutions of N-methylacetamide – The volumetric and compressibility studies between 288.15 and 308.15 K
PublicationApparent molar volumes and apparent molar isentropic compressions of the protein stabilizer, trimethylamine-N-oxide (TMAO) were determined from the densities and speed of sound measured at T = (288.15, 298.15 and 308.15) K in aqueous solutions of N-methylacetamide (NMA) at four different concentrations (2, 4, 6 and 8 mol/kg). The concentration dependencies of the calculated quantities extrapolated to the infinite dilution lead...
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Study on the Positioning Accuracy of the GNSS/INS System Supported by the RTK Receiver for Railway Measurements
PublicationCurrently, the primary method for determining the object coordinates is positioning using Global Navigation Satellite Systems (GNSS) supported by Inertial Navigation Systems (INS). The main goal of this solution is to ensure high positioning availability, particularly when access to satellite signals is limited (in tunnels, areas with densely concentrated buildings and in forest areas). The aim of this article is to determine whether...
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Ductile fracture prediction in thin metallic plates subjected to explosions
PublicationPraca dotyczy modelowania zniszczenia ciągłego. Zaprezentowano wyniki eksperymentów przeprowadzonych na płytach metalowych poddanych eksplozjom oraz wyniki jednoosiowych prób laboratoryjnych. Opisano przyjęty model prawa konstytutywnego oraz kryteriów zniszczenia. Przedstawiono identyfikację parametrów materiałowych dla przyjętego modelu. Zaprezentowano model numeryczny oraz wyniki symulacji które następnie porównano z wynikami...
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High-accuracy computation of hard X-ray focusing and imaging for refractive optics
PublicationA mathematical apparatus for solving problems of X-ray wave propagation through complex optical systems, when the lens thickness can change with jumps, is developed and presented. The developed method is based on the use of the superposition of oriented Gaussian beams, which satisfy the Helmholtz equation with high accuracy. The wave propagation in air and through kinoform and ordinary lenses is considered. Focusing and imaging...
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Simple 2-D Direction-of-Arrival Estimation Using an ESPAR Antenna
PublicationIn this letter, it has been shown how an electronically steerable parasitic array radiator (ESPAR) antenna can be used for 2-D direction-of-arrival (DoA) estimation employing received signal strength (RSS) values only. The proposed approach relies on changes in RSS values recorded at the antenna output port observed for different vertical and horizontal directions, while antenna’s main beam sweeps 360° area around the ESPAR antenna. Based...
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Generation and Characterization of a DNA-GCN4 Oligonucleotide-Peptide Conjugate: The Impact DNA/Protein Interactions on the Sensitization of DNA
PublicationRadiotherapy, the most common therapy for the treatment of solid tumors, exerts its effects by inducing DNA damage. To fully understand the extent and nature of this damage, DNA models that mimic the in vivo situation should be utilized. In a cellular context, genomic DNA constantly interacts with proteins and these interactions could influence both the primary radical processes (triggered by ionizing radiation) and secondary reactions,...
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Reactive imines: Addition of 2-aminopyrimidine to the imine bond and isolation of the aminal from the equilibrium mixture aminal/imine
PublicationThe reaction between o-vanillin and 2-aminopyrimidine leads to the formation of a single crystalline product: aminal, 1, which results from the reaction of the initially formed imine with 2-aminopyrimidine. The reaction was followed by the NMR spectroscopy. VT NMR studies prove that in solution two major species are observed: aminal and imine and their ratio depends on the time or/and temperature with the imine content increasing...
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DYNAMIC RESPONSE OF FORUM GDANSK STRUCTURE DUE TO RAIL TRAFFIC
PublicationThe paper presents the study of the impact of vibration induced by the movement of the railway rolling stock on the Forum Gdańsk structure. This object is currently under construction and is located over the railway tracks in the vicinity of the Gdańsk Główny and Gdańsk Śródmieście railway stations. The analysis covers the influence of vibrations on the structure itself and on the people within. The in situ measurements on existing...
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Effective Air Quality Prediction Using Reinforced Swarm Optimization and Bi-Directional Gated Recurrent Unit
PublicationIn the present scenario, air quality prediction (AQP) is a complex task due to high variability, volatility, and dynamic nature in space and time of particulates and pollutants. Recently, several nations have had poor air quality due to the high emission of particulate matter (PM2.5) that affects human health conditions, especially in urban areas. In this research, a new optimization-based regression model was implemented for effective...
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In the search for experimental and quantumchemical evidence for zwitterionic nature of (2 E )-3-[4-(dimethylamino)phenyl]-2-nitroprop-2-enenitrile – An extreme example of donor–π–acceptor push–pull molecule
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Discussion on “Dynamic soil-structure interaction: A three-dimensional numerical approach and its application to the Lotung case study”. Poor performance of the HSS model
PublicationThe Hardening Soil Small (HSS) is a constitutive model being extension to the well established Hardening Soil Model (HS) accounting for the nonlinearity of small strain stiffness. It is implemented in commercial finite element computer codes for geotechnical analyses and used widely in research and design. The article deals with a problem known as overshooting after very small load reversals. It induces much higher stiffness than...
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Assembly of Lipopolysaccharide in Escherichia coli Requires the Essential LapB Heat Shock Protein
PublicationHere, we describe two new heat shock proteins involved in the assembly of LPS in Escherichia coli, LapA and LapB (lipopolysaccharide assembly protein A and B). lapB mutants were identified based on an increased envelope stress response. Envelope stress responsive pathways control key steps in LPS biogenesis and respond to defects in the LPS assembly. Accordingly, the LPS content in ΔlapB or Δ(lapA lapB) mutants was elevated, with...
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Automated Reduced Model Order Selection
PublicationThis letter proposes to automate generation of reduced-order models used for accelerated -parameter computation by applying a posteriori model error estimators. So far,a posteriori error estimators were used in Reduced Basis Method (RBM) and Proper Orthogonal Decomposition (POD) to select frequency points at which basis vectors are generated. This letter shows how a posteriori error estimators can be applied to automatically select...
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A study on the interaction of rhodamine B with methylthioadenosine phosphorylase protein sourced from an Antarctic soil metagenomic library.
PublicationThe presented study examines the phenomenon of the fluorescence under UV light excitation (312 nm) of E. coli cells expressing a novel metagenomic-derived putative methylthioadenosine phosphorylase gene, called rsfp, grown on LB agar supplemented with a fluorescent dye rhodamine B. For this purpose, an rsfp gene was cloned and expressed in an LMG194 E. coli strain using an arabinose promoter. The resulting RSFP protein was purified...
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Ahmer Bin Hafeez
PeopleI have experience in Microbiology & Computational Biology, particularly bioinformatics, homology modeling, phylogenetics, structural biology, and drug discovery. Currently, my interest lies in translatable omics studies and drug discovery against novel protein targets involved in cancer and infectious diseases and Host-Pathogen PPIs. My aim involves the use of computational methods for the identification of novel targets and to...
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System of monitoring of the Forest Opera in Sopot structure and roofing
PublicationThe authors present a solution realized in Forest Opera (name in Polish: Opera Leśna) in Sopot (Poland) in connection with the modernization and construction of a new roof. The complicated structure of the roof of the facility and the used covering in form of membrane made of technical fabric required (for security reasons) to install the unit of devices allowing for the continuous geodetic monitoring of the facility. Monitoring...
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The Synthesis of 3-Amino-pyrazine-2-carbohydrazide and 3-Amino-N'-methylpyrazine-2-carbohydrazide Derivatives
PublicationW poszukiwaniu biologicznie aktywnych związków otrzymano szereg pochodnych 3-Amino-pirazyno-2-karbohydrazydu i 3-Amino-N'-metylopirazyno-2-karbohydrazydu w wyniku reakcji hydrazydu aminopirazynoinowegokwasu z izocyjanianami, aldehydami, ketonami, CS2 i kwasem mrówkowym.
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The Concept of Accuracy Analysis of the Vertical Displacements Gained from the Hydrostatic Levelling Systems’ Measurements
PublicationAbstract: Nowadays, hydrostatic levelling is a widely used method for the vertical displacements’ determinations of objects such as bridges, viaducts, wharfs, tunnels, high buildings, historical buildings, special engineering objects (e.g., synchrotron), sports and entertainment halls. The measurements’ sensors implemented in the hydrostatic levelling systems (HLSs) consist of the reference sensor (RS) and sensors located on the...
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Survival time prognosis under a Markov model of cancer development
PublicationIn this study we look at a breast cancer data set of women from Pomerania region collected in year 1987-1992 in the Medical University of Gdańsk. We analyze the clinical risk factors in conjunction with Markov model of cancer development. We evaluate Artificial Neural Network (ANN) survival time prediction via a simulation study.
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Tomasz Wąsowicz dr hab.
PeopleTomasz Wąsowicz's research was first related to high-resolution atomic spectroscopy and focused on measurements and analysis of the transition probabilities of the forbidden lines, the hyperfine and isotopic structure of spectral lines of heavy elements, Stark effect in the helium atom. Tomasz Wąsowicz currently studies physicochemical processes occurring during interactions of various forms of radiation with atoms and molecules...
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Remote communication in Scrum teams - a COVID-19 preventive measure or work time optimisation?
PublicationThe article presents the impact of remote work, resulting from the COVID-19 pandemic, on the functioning of Scrum teams. Attempts have been made to analyse the positive and negative aspects of remote work. The article also looks at the impact of remote work on the level of communication and efficiency of Scrum teams. For this purpose, the author conducted research on a sample of 40 organisations that declared to use Scrum methodology,...
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Electrochemical simulation of metabolism for antitumor-active imidazoacridinone C-1311 and in silico prediction of drug metabolic reactions
PublicationThe metabolism of antitumor-active 5-diethylaminoethylamino-8-hydroxyimidazoacridinone (C-1311) has been investigated widely over the last decade but some aspects of molecular mechanisms of its metabolic transformation are still not explained. In the current work, we have reported a direct and rapid analytical tool for better prediction of C-1311 metabolism which is based on electrochemistry (EC) coupled on-line with electrospray...
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...
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The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model
PublicationDespite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind,...