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Structural analysis and predicting effects of natural mutations on telomerase
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Molecular basis and quantitative assessment of TRF1 and TRF2 protein interactions with TIN2 and Apollo peptides
PublikacjaShelterin 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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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation
PublikacjaEmrE 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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Identification of 1H‐indene‐(1, 3, 5, 6)‐tetrol derivatives as potent pancreatic lipase inhibitors using molecular docking and molecular dynamics approach
PublikacjaPancreatic lipase is a potential therapeutic target to treat diet-induced obesity in humans, as obesity-related diseases continue to be a global problem. Despite intensive research on finding potential inhibitors, very few compounds have been introduced to clinical studies. In this work, new chemical scaffold 1H-indene-(1,3,5,6)-tetrol was proposed using knowledge-based approach, and 36 inhibitors were derived by modifying its...
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Docking simulations, Molecular properties and ADMET studies of novel Chromane6,7diol analogues as potential inhibitors of Mushroom tyrosinase
PublikacjaResearch on inhibition of tyrosinase enzyme has attained significant value, because tyrosinase inhibitors have potential applications in medicine, cosmetics (as whitening agents) and in agriculture (as bioinsecticides). Determination and elucidation of new tyrosinase inhibitors are not only beneficial for medical purposes, but their promising applications in improving food quality and nutritional...
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublikacjaEmrE 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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Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds
PublikacjaReverse transcriptase (RT) inhibitors are currently used to treat human immunodeficiency virus (HIV)-1 infections. In this work, novel triethylamine derivatives were designed and studied by rigid and flexible docking and molecular dynamics (MD) approaches. An apo form of HIV-1 RT was also studied by MD simulation to analyze comparative response of protein in ligand-bound and ligand-unbound forms. Among newly designed HIV-1 RT inhibitors,...
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The structurally similar TRFH domain of TRF1 and TRF2 dimers shows distinct behaviour towards TIN2
PublikacjaThe telomere repeat binding-factor 1 and 2 (TRF1 and TRF2) proteins of the shelterin complex bind to duplex telomeric DNA as homodimers, and the homodimerization is mediated by their TRFH (TRF-homology) domains. We performed molecular dynamic (MD) simulations of the dimer forms of TRF1TRFH and TRF2TRFH in the presence/absence of the TIN2TBM (TIN2, TRF-interacting nuclear protein 2, TBM, TRF-binding motif) peptide. The MD results...
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Extracting functional groups of ALLINI to design derivatives of FDA‐approved drugs: Inhibition of HIV‐1 integrase
PublikacjaHIV‐1 integrase (IN) is crucial for integration of viral DNA into the host genome and a promising target in development of antiretroviral inhibitors. In this work, six new compounds were designed by linking the structures of two different class of HIV‐1 IN inhibitors (active site binders and allosteric IN inhibitors (ALLINIs)). Among newly designed compounds, INRAT10b was found most potent HIV‐1 IN inhibitor considering different...
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Structural, functional, and stability change predictions in human telomerase upon specific point mutations,
PublikacjaOverexpression of telomerase is one of the hallmarks of human cancer. Telomerase is important for maintaining the integrity of the ends of chromosomes, which are called telomeres. A growing number of human disease syndromes are associated with organ failure caused by mutations in telomerase (hTERT or hTR). Mutations in telomerase lead to telomere shortening by decreasing the stability of the telomerase complex, reducing its accumulation,...
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O zbieżności rozwiązań w nieliniowym mikropolarnym ośrodku sprężysto-plastycznym - zastosowanie elementów skończonych wyższego rzędu.
PublikacjaEfekty lokalizacji w nieliniowym geometrycznie sprężysto-plastycznym mikropolarnym ośrodku z osłabieniem materiału. Hipotezy Hubera-Misesa-Hencky’ego i Druckera-Pragera. Rozwiązanie równań sprężysto-plastycznych przy użyciu algorytmu powrotnego. Opis zastosowanych elementów skończonych. Przykłady numeryczne obliczeń w geotechnice.
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Architektura bezpieczeństwa systemu netBaltic
PublikacjaW artykule zaprezentowano założenia dotyczące zabezpieczania węzłów sieci realizowanej w ramach systemu netBaltic. Ze względu na dużą różnorodność rozważanych mechanizmów komunikacyjnych architektura bezpieczeństwa została podzielona na kilka elementów – infrastrukturę klucza publicznego (PKI), bezpieczeństwo systemowe węzłów, zabezpieczanie komunikacji w modelu samoorganizującej wieloskokowej sieci kratowej, a także sieci niewrażliwej...
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A decade of Poland`s integrated Road Safety Programme - economic develop-ment vs. road unsafety. W: [CD-ROM]. Conference proceedings. SORIC´02. 2nd Safety on Road Internationaload International Conference. Kingdom of Bah- rain, 21-23 October 2002. Bahrain: CTRS Univ. Bahrain**2002 [8 s. 5 rys. bibliogr. 5 poz. 10 lat Krajowego Programu Bezpieczeństwa Ruchu Drogowego w Polsce - rozwój ekonomiczny a niebezpieczeństwo ruchu.
PublikacjaReferat zawiera analizę doświadczeń z dziesięciu lat pracy oraz wdrożeń Kra-jowego Programu Bezpieczeństwa Ruchu Drogowego GAMBIT. Przedstawia również analizę przyczyn gwałtownego spadku liczby- śmiertelnych ofiar wypadków dro-gowych w Polsce w roku 2001.
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Program komputerowy do odtwarzania kształtu osi toru kolejowego
PublikacjaW pracy przedstawiono metodę odtwarzania kształtu osi toru kolejowego w płaszczyźnie poziomej na podstawie ciągłych pomiarów satelitarnych. W metodzie tej został wykorzystany algorytm projektowania odcinków trasy kolejowej położonych w łuku, w którym zastosowano analityczną formę opisu za pomocą odpowiednich formuł matematycznych. Procedura projektowania ma charakter uniwersalny − stwarza możliwość zróżnicowania rodzaju i długości...
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Optimization of Energetic Train Cooperation
PublikacjaIn the article, possible ways of using energy recovered during regenerative braking of trains are presented. It is pointed out that the return of recovered electricity directly to the catenary and its use in the energy cooperation of vehicles can be a no-cost method (without additional infrastructure). The method of energy cooperation between trains and its main assumptions, that uses the law of conservation of energy, are described...
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Multiscale model for blood flow after a bileaflet artificial aortic valve implantation
PublikacjaCardiovascular diseases are the leading cause of mortality in the world, mainly due to atherosclerosis and its consequences. The article presents the numerical model of the blood flow through artificial aortic valve. The overset mesh approach was applied to simulate the valve leaflets motion and to realize the moving mesh, in the aortic arch and the main branches of cardiovascular system. To capture the cardiac system’s response...
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Design analysis of ORC micro-turbines making use of thermal energy of oceans
PublikacjaThe article presents the results of the analysis of energy conversion cycles making use of thermal energy of oceans. The objects of analysis were two cases of closed Organic Rankine Cycle (ORC) power plants, which were: the cycle in which the vapour of the working medium was produced by warm oceanic water in the circum-equatorial zone, and the so-called “arctic” cycle in which this vapour was produced by non-frozen water in the circumpolar...
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Predicting cutting power for band sawing process of pine and beech wood dried with the use of four different methods
PublikacjaWood drying is an important stage in the woodworking process. After drying, wood is subject to a re-sawing process, for which a high quality surface, low material loss, and high efficiency are often required. In this paper, forecasted values were presented of cutting power for the re-sawing process of pine and beech wood that were dried with four different methods. Forecasting of cutting power for an industrial band saw machine...
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Searching for road deformations using mobile laser scanning
PublikacjaMillions of people use roads every day all over the world. Roads, like many other structures, have an estimated durability. In Poland a lot of the roads were built at the turn of the 20th and 21st c., especially for light cars. Many of these roads carry traffic and heavy goods vehicles which were not predicted when the traffic was first estimated. It creates a lot of problems with technical conditions and the infrastructure must...
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Metody zwiększania dostępności i efektywności informatycznej infrastruktury w inteligentnym mieście
PublikacjaW pracy omówiono metody zwiększania dostępności i efektywności informatycznej infrastruktury w inteligentnym mieście. Sformułowano dwa kryteria do oceny rozmieszczenia kluczowych zasobów w systemie smart city. Zobrazowano proces wyznaczania rozwiązań kompromisowych spośród rozwiązań Pareto-optymalnych. Omówiono metaheurystyki inteligencji zbiorowej, w tym roju cząstek, kolonii mrówek, roju pszczół oraz ewolucji różnicowej, za pomocą...
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Modelling of Geared Multi-Rotor System
PublikacjaIn the paper the method of modelling a speed-varying geared rotor system is presented. The proposed approach enables us to obtain an accurate low-order lumped parameter representation of the investigated system. The final model consists of reduced modal models of an undamped beam/torsional shaft system as well as a spatially lumped model of other linear and nonlinear phenomena including gear mesh interaction.
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A concept of measurement system based on the Z-Wave standard
PublikacjaIn the paper a new concept of measurement system based on the Z-Wave standard is presented. This standard is dedicated to use mainly in home automation systems, but its properties enable to use it in dispersed measurement systems and support wireless communication between measurement nodes in a mesh-type network. In the paper basic metrological aspects of the Z-Wave standard and an example of impedance measurement system are discussed.
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Mobile monitoring system for gaseous air pollution
PublikacjaThe concept of a mobile monitoring system for chemical agents control in the air is presented. The proposed system can be applied to measure industrial and car traffic air pollution. A monitoring station is relatively small and can be placed on cars or public transportation vehicles. Measured concentrations of air pollutants are collected and transferred via the GSM network to a central data base. Exemplary results from a measurement...
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Malarstwo
PublikacjaAutor, mieszkając od wielu lat na dwóch krańcach Europy, postrzega swoje życie w kategoriach ''podróży''. Podróży rozpiętej między Północą a Południem, pomiędzy domami, miejscami, pomiędzy lądami i morzami, ale także podróży w czasie, gdy dociera do miejsc pamiętających czasy Imperium Rzymskiego czy ekspansji Maurów na Półwyspie Iberyjskim. Wystawa prezentuje graficzny wymiar tych podróży uchwycony w szkicach, rysunkach i malarstwie.
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Hybrid biobateryy based on arylated carbon nanotubes and laccase
PublikacjaSingle-walled carbon nanotubes (SWCNT) were covalently modified with antracene and antraquinone and used for the construction of cathodes for biocatalytic reduction od dioxygen. The nanotubes with aromatic groups casted onto the electrode increased the working surface of the electrode and enabled efficient direct electron tarnsfer (DET) between the enzyme and the electrode. the aryl groups enter the hydrophobic pocket of the T1...
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Mechanizmy bezpieczeństwa w strefie C systemu netBaltic
PublikacjaW artykule zaprezentowano rozwiązania zaimplementowane do zabezpieczania komunikacji w warunkach sporadycznej i nieciągłej łączności (Delay Tolerant Networking – DTN) w systemie netBaltic - charakterystycznej dla strefy C tego systemu. Ze względu na dużą różnorodność rozważanych mechanizmów komunikacyjnych, architektura bezpieczeństwa całego systemu została podzielona na kilka elementów – infrastrukturę klucza publicznego (PKI),...
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Methodology of generation of CFD meshes and 4D shape reconstruction of coronary arteries from patient-specific dynamic CT
PublikacjaDue to the difficulties in retrieving both the time‑dependent shapes of the vessels and the generation of numerical meshes for such cases, most of the simulations of blood flow in the cardiac arteries use static geometry. The article describes a methodology for generating a sequence of time‑dependent 3D shapes based on images of different resolutions and qualities acquired from ECG‑gated coronary artery CT angiography. The precision...
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Integration of thermographic data with the 3D object model
PublikacjaThe aim of the paper is to present new method for merging the 3D model data of the measured object with thermograms. Our technique is based on the combination of visual 3D imaging technique and thermal imaging technique, which maps the 2D thermograms on to 3D anatomical mesh model. The combination of these imaging modalities allows the generation of combined 3D and thermal data from which thermal signatures can be verified and...
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Chłodzenie słońcem
PublikacjaNiektóre możliwości chłodzenia i klimatyzacji pomieszczeń, o których mowa w artykule, przy wykorzystaniu energii słonecznej, mogą być realizowane w różnych wariantach, co jest dokonywane w zastosowaniach praktycznych. Zaletą systemów opartych na chłodzeniu pomieszczeń wykorzystujących energię promieniowania słonecznego jest to, że są one użyteczne w tym czasie, gdy do powierzchni Ziemi dociera duża ilość energii słonecznej kiedy...
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LABORATORY STAND FOR INVESTIGATIONS OF THE QUICK - CHANGING TEMPERATURE OF GAS FLOWING IN THE PISTON COMPRESSOR OUTLET CHANNEL
PublikacjaThis paper presents a laboratory stand, created as a part of work on the doctor dissertation, intended for investigation of heat and flow processes taking place in the Espholin H3S piston compressor outlet channel. The test stand elements and their configuration within the stand are described. Discussed are also problems connected with the quick-changing measurement technique, solutions which have been proposed so far in that technology...
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Tris(1,10-phenanthroline-k2N,N')iron(II) dichloride methanol hexasolvate
PublikacjaTytułowy związek składa się z kompleksowego kationu, w którym do żelaza(II) oktaedrycznie koordynują trzy bidentne ligandy fenantrolinowe oraz dwóch jednoujemnych agregatów: [Cl(MeOH)2](-) i [Cl(MeOH)4](-), gdzie jony chlorkowe i cząsteczki metanolu są powiązane wiązaniami wodorowymi.
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Cleaner energy for sustainable future using hybrid photovoltaics-thermoelectric generators system under non-static conditions using machine learning based control technique
PublikacjaIn addition to the load demand, the temperature difference between the hot and cold sides of the thermoelectric generator (TEG) module determines the output power for thermoelectric generator systems. Maximum power point tracking (MPPT) control is needed to track the optimal global power point as operating conditions change. The growing use of electricity and the decline in the use of fossil fuels have sparked interest in photovoltaic-TEG...
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Resilient Routing in Communication Networks
PublikacjaThis important text/reference addresses the latest issues in end-to-end resilient routing in communication networks. The work highlights the main causes of failures of network nodes and links, and presents an overview of resilient routing mechanisms, covering issues related to the Future Internet (FI), wireless mesh networks (WMNs), and vehicular ad-hoc networks (VANETs). For each of these network architectures, a selection of...
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LOW NOISE TIRES FOR HYBRID AND ELECTRIC VEHICLES
PublikacjaLow Emission Vehicles that are hybrid and electric cars may benefit from specially designed tires that are optimized for driving conditions typical for such vehicles. It is possible that in the future Low Emission Vehicles, especially passenger cars, will substitute conventional vehicles in all applications, however for the time being they are mostly used in urban and suburban areas. Urban traffic has a rather low demand for grip...
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Mobility Oriented Development (MOD): Public-Private Partnership in Urban Parking & Traffic Management with the Use of Autonomous Automobiles, Car-Sharing, Ridesharing Modes of Transport & Mobility as a Service (MaaS)
PublikacjaThe focus of the following research are relations between mobility technologies and metropolitan (urban and suburban) spatial structures. In this paper the author discusses various urban modes of transport (automobile, mass transit) in the context of emerging technical (autonomous vehicles, self-driving cars and driverless shuttles) and organizational (carpooling, ridesharing, car-sharing, on-demand mobility) solutions for " mobility...
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Combined environmental testing device for picosatellites
PublikacjaAs access to space conditions becomes more available, both technically and economically, scientists’ interest in launching finer and more sophisticated experiments grows. To be qualified for launch, such experiments need to be carefully tested prior to the event. The tests should represent actual launch conditions as closely and in a detailed manner. Typical tests for payload include: vibration tests, thermal and vacuum tests,...
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A procedure for elastoplastic hardening function identification.
PublikacjaThe inverse analysis method for identifying a nonlinear hardening function,which governs a plastic yielding of soil and rock materials in the framework of elastoplastic theory is presented. A concept of two stage finite element based on spatial discretization of computational space and hardening function space is introduced. The proposed inverse analysis can be classified as the output least squares method. The Levenberg Marquard...
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Possibility of thermal imaging use in studies of natural convection heat transfer on the example of an isothermal vertical plate.
PublikacjaA new method of infrared (IR) camera use in convective heat transfer studies has been presented. Until now, IR cameras were utilized for temperature field visualizations of flat heated surfaces of solid objects only. Because liquids and gasses do not emit radiation in the infrared range of wave lengths, detection of temperature field in the air was conducted with the use of plastic mesh, which, after heating by hot air, emits infrared...
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Computer-aided reconstruction of the railway track axis geometrical shape
PublikacjaIn the paper a method of the railway track axis geometrical shape identification in a horizontal plane, directly from the continuous satellite measurements, is presented. In this method, an algorithm for the design of railway track sections located in the horizontal arc is used. The algorithm uses an analytical description of the layout by means of suitable mathematical formulas. The design procedure has a universal character and...
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Application of the Optimization Methods to the Search of Marine Propulsion Shafting Global Equilibrium in Running Condition
PublikacjaFull film hydrodynamic lubrication of marine propulsion shafting journal bearings in running condition is discussed. Considerable computational difficulties in non-linear determining the quasi-static equilibrium of the shafting are highlighted. The approach using two optimization methods (the particle swarm method and the interior point method) in combination with the specially developed relaxation technique is proposed to overcome...
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Optimal Placement of Phasor Measurement Unit in Power System using Meta-Heuristic Algorithms
PublikacjaThe phasor measurement units (PMUs) play an important and vital role in power system monitoring and controlling, since they provide the power system phasors stamped with a common real time reference through a global positioning system (GPS). Indeed, from economical point of view it is not possible to set PMUs in all system buses due to the high cost and the requirement of more complex communication...
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Projektowanie układów geometrycznych toru z zastosowaniem optymalizacji wielokryterialnej
PublikacjaW pracy przedstawiono metodę projektowania odcinków trasy kolejowej położonych w łuku, dostosowaną do techniki mobilnych pomiarów satelitarnych. Rozwiązanie problemu projektowego wykorzystuje zapis matematyczny i polega na wyznaczeniu uniwersalnych równań opisujących całość układu geometrycznego. Odbywa się to sekwencyjnie, obejmując kolejne fragmenty tegoż układu. Procedura projektowania ma charakter uniwersalny, gdyż w ogólnym...
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Development of Local IDF-formula Using Controlled Random Search Method for Global Optimization
PublikacjaThe aim of the study is to present the effective and relatively simple empirical approach to rainfall Intensity-Duration-Frequency-formulas development, based on Controlled Random Search (CRS) for global optimization. The approach is mainly dedicated to the cases in which the commonly used IDF-relationships do not provide satisfactory fit between simulations and observations, and more complex formulas with higher number of parameters...
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Możliwości zamiany elektrycznych przepływomierzy powietrza stosowanych w silnikach spalinowych samochodów
PublikacjaW artykule przedstawiono podstawowe typy przepływomierzy powietrza, stosowane w silnikach spalinowych samochodów: z klapąspiętrzającą, HLM, HFM, Vortex i MAP. Przedstawiono wyniki badania tych przepływomierzy na specjalnie przygotowanym stanowisku pomiarowym. Przeanalizowano możliwość ich zamiany i zweryfikowano taką możliwość w praktyce.
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Molecular docking studies towards development of novel Gly-Phe analogs for potential inhibition of Cathepsin C (dipeptidyl peptidase I).
PublikacjaCathepsin C is a cysteine protease required for activation of various pro-inflammatory serine proteases and, essentially, is of interest as a therapeutic target. Cathepsin C coordinate system was employed as a model to study the interaction of some already available inhibitors of Cathepsin C. Compounds containing Gly-Phe fragment with functional groups at its ends were designed by knowledge based approach. Using AutoDock and...
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Recognition Dynamics of Cancer Mutations on the ERp57-Tapasin Interface
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SiMiSnoRNA: Collection of siRNA, miRNA, and snoRNA database for RNA Interference
PublikacjaObjective:The discovery of sequence specific gene silencing which occurs due to the presence of double-stranded RNAs has considerable impact on biology, revealing an unknown level of regulation of gene expression. This process is known as RNA interference (RNAi) or RNA silencing in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecule. Two types of small RNA molecules - small...
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COMPUTER-AIDED DESIGN OF ORGANOPHOSPHORUS INHIBITORS OF UREASE
PublikacjaBased on the structure of the most potential inhibitor diamidophosphate, various novel groups of inhibitors were developed by knowledge-based design approach with covalent carbon-phosphorus or carbon-phosphorus-carbon bond to improve hydrolytic stability to inhibit the microbial ureases. Designed compounds were evaluated with 10 (LigScore1, LigScore2, PLP1, PLP2, JAIN, PMF, PMF04, LUDI_1, LUDI_2 and LUDI_3) different scoring functions...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublikacjaLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...
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EXPERIMENTS AND SIMULATIONS FOR LAPAROSCOPICVENTRAL HERNIA REPAIR IMPROVEMENT
PublikacjaThe authors conducted a wide experimental and numerical study in order to determine effective approaches in the laparoscopic VH repair. At first the study covered identification of mechanical properties of the abdominal fascia, implants, tacks and transabdominalsutures. Basis on these data, the one and two-dimensional mathematical models were formulated and a number of numerical static and dynamic analyses were carried out. Then...