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Search results for: casp, covid, ema, model accuracy, protein structure prediction, sars-cov-2
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Crystal Growth, Structure, and Magnetism of the 2D Spin 1/2 Triangular Lattice Material Rb3Yb(PO4)2
PublicationThe single-crystal growth, crystal structure, heat capacity, and anisotropic magnetization characterization of Rb3Yb- (PO4)2, a Yb-based triangular lattice material, are presented. Single-crystal X-ray diffraction shows that Rb3Yb(PO4)2 exhibits [Yb(PO4)]∞ layers, with the Yb in an ordered plane of equilateral triangles. One phosphate group oxygen that is not a near neighbor of the magnetic Yb displays positional disorder. The...
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Machine learning-based prediction of seismic limit-state capacity of steel moment-resisting frames considering soil-structure interaction
PublicationRegarding the unpredictable and complex nature of seismic excitations, there is a need for vulnerability assessment of newly constructed or existing structures. Predicting the seismic limit-state capacity of steel Moment-Resisting Frames (MRFs) can help designers to have a preliminary estimation and improve their views about the seismic performance of the designed structure. This study improved data-driven decision techniques in...
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The 2:1 cocrystal of benzamide and pentafluororbenzoic acid
PublicationKrystaliczna struktura centrosymetrycznej supermolekuły składa się z czterech cząsteczek benzamidu oraz dwóch kwasu karboksylowego, które powiązane są ze sobą za pomocą wiązań wodorowych typu O-H...O oraz N-H...O.
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User satisfaction model
PublicationRaport techniczny - opis metody ''User Satisfaction Methods'' wykorzystywanej w projektowaniu komunikacji człowiek-komputer oraz doskonaleniu interfejsu użytkownika.
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Rating Prediction with Contextual Conditional Preferences
PublicationExploiting contextual information is considered a good solution to improve the quality of recommendations, aiming at suggesting more relevant items for a specific context. On the other hand, recommender systems research still strive for solving the cold-start problem, namely where not enough information about users and their ratings is available. In this paper we propose a new rating prediction algorithm to face the cold-start...
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A Hierarchical Multiscale Approach to Protein Structure Prediction: Production of Low‐Resolution Packing Arrangements of Helices and Refinement of the Best Models with a United‐Residue Force Field
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Effect of temperature and composition on physical properties of deep eutectic solvents based on 2-(methylamino)ethanol – measurement and prediction
PublicationNovel deep eutectic solvents were synthesized using 2-(methylamino)ethanol as hydrogen bond donor with tetrabutylammonium bromide or tetrabutylammonium chloride or tetraethylammonium chloride as hydrogen bond acceptors. Mixtures were prepared at different molar ratios of 1:6, 1:8 and 1:10 salt to alkanolamine and then Fourier Transform Infrared Spectroscopy measurements were performed to confirm hydrogen bonds interactions between...
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The circular chromatic index of some class 2 graphs
PublicationW artykule został wyznaczony cyrkularny indeks chromatyczny dla dwóch rodzin grafów klasy 2. Co więcej, podano nie trywialne oszacowania tego parametru dla snarków Isaacsa i Goldberga. Na koniec artykułu rozważana jest złożoność obliczeniowa problemów związanych z cyrkularnym kolorowaniem krawędzi.
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A simple model of circular hydraulic pump
PublicationRozpatrzono warunki powstawania osiowosymetrycznego uskoku hydraulicznego. Przedstawiono model, w którym rozpatrzono obecność dodatkowych strat w równaniu Bernoulliego. Przyczyniają się one do powstawania dodatkowego wiru w miejscu uskoku. Porównanie z wynikami badań eksperymentalnych potwierdza słuszność przyjętych tez.
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Wood structure constraints on sawing accuracy with narrow-kerf saws
PublicationW pracy przedstawiono analizę przyczyn i przykłady niedokładności przecinania wynikających z lokalnych zmian struktury drewna.
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Działania antykryzysowe w obszarze kultury w trakcie pandemii SARS-CoV-2. Stan obecny i wnioski de lege ferenda w zakresie zwiększenia partycypacji obywatelskiej oraz instytucjonalnej
PublicationCelem artykułu jest analiza różnych rozwiązań prawnych w zakresie wsparcia instytucji kultury w trakcie stanu epidemii. Przeprowadzono przegląd działań Ministerstwa Kultury i Dziedzictwa Narodowego wspierających instytucje kultury w Polsce w czasie epidemii według stanu na maj 2020 r. Na podstawie analizy wskazano wnioski de lege ferenda co do nowych możliwości finansowania działań takich instytucji. Autorzy prezentują rozwiązania...
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Copper containing protein sites - structure, properties and models
PublicationEnzymy organizmów żywych katalizują wiele reakcji stosowanych w przemyśle chemicznym. Przykładem potencjalnego zastosowania enzymu w produkcji jest synteza L-Dopy przy udziale tyrozynazy. Ze względu na możliwe praktyczne zastosowanie w katalizie, otrzymano i opisano wiele prostych modeli miejsc aktywnych enzymów. W artykule opisano niektóre modele białek zawierających miedź.
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On the Origin of Protein Superfamilies and Superfolds
PublicationDistributions of protein families and folds in genomes are highly skewed, having a small number of prevalent superfamiles/superfolds and a large number of families/folds of a small size. Why are the distributions of protein families and folds skewed? Why are there only a limited number of protein families? Here, we employ an information theoretic approach to investigate the protein sequence-structure relationship that leads to...
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Polysaccharide–Protein Complexes in a Coarse-Grained Model
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Reactions of R2P-P(SiMe3)2 with [(R'3P)2PtCl2]. Syntheses and Structures of [μ2-(1,2:2-η-P2){Pt(PEt3)2}2{Pt(PEt3)2Cl}]+Cl-, [{(Et2PhP)2Pt}2P2], [{(p-Tol3P)2Pt}2P2] and [(p-Tol3P)ClPt(μ-PPh2)2Pt(p-Tol3P)Cl]
PublicationReakcje difosfanów R2P-P(SiMe3)2 z [(R'3P)2PtCl2] są bardzo złożone. Główną ścieżką reakcji jest rozszczepienie wiązania P-P w startowym R2P-P(SiMe3)2, po czym następuje utworzenie kompleksu zawierającego P2: [{(R'3P)2Pt}2P2] oraz difosfanu R2P-PR2. Produkty reakcji (zarówno główne jak i uboczne), zostały scharakteryzowane na podstawie spektroskopii 31P NMR. Dla czterech tytułowych związków wykonano rentgenowską analizę strukturalną...
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Spirometry measurement model - the diagnostic purpose support
Publicationthe paper presents a new model of respiratory mechanism based on the spirometry measurements. the spirometry test assesses the efficiency of the lung ventilation. the respiratory system functioning is based on the ventilation mechanism. thus the quality of the lung depends on the quality of lung ventilation. modelling of the respiratory system supports a diagnostic process. the model parameter estimates are obtained on the basis...
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Delay induced oscillations in gene expression of Hes1 protein model
PublicationW pracy został omówiony model produkcji białka Hes1. Stężenie Hes1 jest kontrolowane przez ujemne sprzężenie zwrotne wbudowane w białko i jego mRNA. Przeprowadzona analiza potwierdziła znane wyniki numeryczne, że oscylacje wywołane są przez opóźnienie. Pokazaliśmy również, że jeśli współczynnik Hilla jest większy niż 1, to istnieje krytyczna wartość opóźnienia, dla której ma miejsce bifurkacja Hopfa i pojawiają się rozwiązania...
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Ammine(2-ethylpyridine-κN)bis(tri-tert-butoxysilanethiolato-κS)cobalt(II)
PublicationTytułowy związek [Co(C12H27O3SSi)2(C7H9N)(NH3)] został otrzymany w reakcji dimerycznego amoniakalnego tri-tert-butoksysilanotiolanu kobaltu(II) z 2-etylopirydyną. Atom kobaltu w otrzymanym związku jest koordynowany przez dwa atomy siarki, jedną resztę 2-etylopirydyny i jedną cząsteczkę amoniaku. Dzięki specyficznemu przestrzennemu ustawieniu ligandów, dodatkowo tworzy się wiązanie wodorowe wewnątrz cząsteczkowe N-H - S
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Electronic structure and rovibrational predissociation of the 2^1Π state in KLi
PublicationAdiabatic potential energy curves of the 3^1Σ^+, 3^3Σ^+, 2^1Π and 2^3Π states correlating for large internuclear distance with the K(4s) + Li(2p) atomic asymptote were calculated. Very good agreement between the calculated and the experimental curve of the 2^1Π state allowed for a reliable description of the dissociation process through a small (∼20 cm−1 for J = 0) potential energy barrier. The barrier supports several rovibrational...
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Application of MARKAL model to optimisation of electricity generation structure in Poland in the long-term time horizon Part I - concept of the model
PublicationIn this paper, which inaugurates a series of papers on this subject, a concept is proposed of a power system development model with regard to the technological structure of electricity generation in Poland, in the long-term time perspective – until 2060. The model is based on the mathematical structure of the MARKAL optimization package. The paper presents a brief description of the tool used in the model research. In addition,...
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublicationThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
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Assessment of Grassland Biomass Prediction Using AquaCrop Model: Integrating Sentinel-2 Data and Ground Measurements in Wielkopolska and Podlasie Regions, Poland
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A Quality Model for UML tools
PublicationJakość narzędzi UML wpływa na efektywność wykonywania zadań związanych z modelowaniem systemów w procesie wytwarzania oprogramowania. Celem badań prezentowanych w tym referacie jest wyodrębnienie kryteriów jakości narzędzi UML. Omówiono rolę narzędzi UML w projekcie informatycznym, a następnie zaprezentowano szereg kryteriów jakości narzędzi UML wraz z aspektami oceny oraz opisem ankiety, która służy do oceny narzędzi względem...
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The elasto-viscoplstic Chaboche model
PublicationW artykule przedstawiono rozwoj i numeryczną aplikacje sprężysto-lepkoplastycznego modelu Chabocha. Przedstawione są także szczegółowe opisy kilkunastu wariantów modelu Chaboche'a wraz z parametrami materiałowymi.
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Classification of Covid-19 using Differential Evolution Chaotic Whale Optimization based Convolutional Neural Network
PublicationCOVID-19, also known as the Coronavirus disease-2019, is an transferrable disease that spreads rapidly, affecting countless individuals and leading to fatalities in this worldwide pandemic. The precise and swift detection of COVID-19 plays a crucial role in managing the pandemic's dissemination. Additionally, it is necessary to recognize COVID-19 quickly and accurately by investigating chest x-ray images. This paper proposed a...
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A model of stealth maritime object having some innovative solutions concerning the object form, structure and materials.
Open Research DataThe aim of the project is to work out a model of the stealth maritime object which will have innovative solutions concerning the object form, structure and materials. These solutions should enable a modification of combinations of the object features defining the object stealth characteristics (difficulty of the object detection in the water). It is...
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Personalized prediction of the secondary oocytes number after ovarian stimulation: A machine learning model based on clinical and genetic data
PublicationControlled ovarian stimulation is tailored to the patient based on clinical parameters but estimating the number of retrieved metaphase II (MII) oocytes is a challenge. Here, we have developed a model that takes advantage of the patient’s genetic and clinical characteristics simultaneously for predicting the stimulation outcome. Sequence variants in reproduction-related genes identified by next-generation sequencing were matched...
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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
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Novel 2-(2-alkylthiobenzenesulfonyl)-3-(phenylprop-2-ynylideneamino)guanidine derivatives as potent anticancer agents – Synthesis, molecular structure, QSAR studies and metabolic stability
PublicationA series of new 2-(2-alkylthiobenzenesulfonyl)-3-(phenylprop-2-ynylideneamino)guanidine derivatives have been synthesized and evaluated in vitro by MTT assays for their antiproliferative activity against cell lines of colon cancer HCT-116, cervical cancer HeLa and breast cancer MCF-7. The obtained results indicated that these compounds display prominent cytotoxic effect. The best anticancer properties have been observed for derivatives...
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High accuracy hydroacoustic system to study codend model parameters
PublicationWażnym zadaniem projektantów narzędzi połowowych jest stworzenie efektywnych narzędzi połowowych działających selektywnie poprzez optymalizacje ich geometrii. Hydroakustyczny system pomiaru geometrii modeli worków dorszowych opisany w artykule został zaprojektowany dla opracowania konstrukcji worka dorszowego na potrzeby rybołówstwa na Morzu Bałtyckim.System składa się z 10 par przetworników ultradźwiękowych, mikroprocesorowego...
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The structure of knowledge resources supporting a model of IT technologies architecture = Struktury zasobów wiedzy wspierających model architektury technologii IT
PublicationThis paper introduces an abstract model for tools used in the software engineering process. The main goal of the research is to develop a universal model which allows a description of tools used in the process. The model supports a decision making process and gives an option to choose the best tooling for the situation. The model considers many factors including, but not exclusive to, the company structure, project environment...
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boundary 2
Journals -
Joanna Raczek dr inż.
PeopleEmployment 2003 -- 2019: Faculty of Applied Physics and Mathematics, Gdańsk University of Technology. 2019 - present: Faculty of Electronic, Informatics and Telecominications, Gdańsk University of Technology. Education May 2007: Doctor of Philosophy in Mathematics, University of Gdańsk. Doctoral dissertation: "Paired domination and doubly domination in graphs". Supervisor: dr hab. Jerzy Topp. 2000 -- 2004 Bachelor of Science...
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublicationThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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Redox State Sensitive Spectroscopy of the Model Compound [(H-dcbpy)(2)Ru-II(NCS)(2)](2-) (dcbpy=2,2 '-Bipyridine-4,4 '-dicarboxylato)
PublicationThe charge transfer reaction mechanism in a ruthenium polypyridine model complex with isothiocyanato ligands, i.e., [(H-dcbpy)(2)Ru(NCS)(2)](2-) 2Bu(4)N(+) (Ru2H) (dcbpy = 2,2'-bipyridine-4,4'-dicarboxylato), has been investigated by combining UV-vis absorption, resonance Raman spectroscopy, and electrochemical methods. Understanding the photophysics of light-harvesting complexes of this class is an indispensable prerequisite to...
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Modelling gene expression of a self-regulating protein
PublicationWe analyze a model of gene transcription and protein synthesis. We take into account the number of sites on the protein’s promoter at which the protein’s dimers can bind blocking transcription of protein mRNA.
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Improving the Accuracy in Sentiment Classification in the Light of Modelling the Latent Semantic Relations
PublicationThe research presents the methodology of improving the accuracy in sentiment classification in the light of modelling the latent semantic relations (LSR). The objective of this methodology is to find ways of eliminating the limitations of the discriminant and probabilistic methods for LSR revealing and customizing the sentiment classification process (SCP) to the more accurate recognition of text tonality. This objective was achieved...
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High quality speech codec employing sines+noise+transients model
PublicationA method of high quality wideband speech signal representation employing sines+transients+noise model is presented. The need for a wideband speech coding approach as well as various methods for analysis and synthesis of sines, residual and transient states of speech signal is discussed. The perceptual criterion is applied in the proposed approach during encoding of sines amplitudes in order to reduce bandwidth requirements and...
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Algebraic periods of self-maps of a rational exterior space of rank 2
PublicationArtykuł stanowi kompletny opis okresów algebraicznych dla odwzorowań wymiernej przestrzeni zewnętrznej rangi 2 w siebie.
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Minimal parameter implicit solvent model for ab initioelectronic-structure calculations
PublicationAbstract - We present an implicit solvent model for ab initio electronic-structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comput. Chem., 23 (2002) 662). While this model depends on only two parameters, we demonstrate...
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Novel primosomal protein B from thermophilic bacterium Thermoanerobacter tengcongensis
PublicationWe report the identification and characterization of theprimosomal protein B (PriB) from thermophilic bacteriumThermoanerobacter tengcongensis (TtePriB). It is the largestknown bacterial PriB protein consisting 216 amino acidresidues with a calculated molecular mass of 25 kDa. Surprisingly,it is functional as monomer containing two single-stranded DNA binding domain (OB-fold) and it is thecompletely new kind structure of SSB protein....
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Evaluating Performance and Accuracy Improvements for Attention-OCR
PublicationIn this paper we evaluated a set of potential improvements to the successful Attention-OCR architecture, designed to predict multiline text from unconstrained scenes in real-world images. We investigated the impact of several optimizations on model’s accuracy, including employing dynamic RNNs (Recurrent Neural Networks), scheduled sampling, BiLSTM (Bidirectional Long Short-Term Memory) and a modified attention model. BiLSTM was...
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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublicationThe UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template...
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Characterization of a single-stranded DNA-binding-like Protein from Nanoarchaeum equitans - a nucleic acid binding protein with broad substrate specificity
PublicationBackground SSB (single-stranded DNA-binding) proteins play an essential role in all living cells and viruses, as they are involved in processes connected with ssDNA metabolism. There has recently been an increasing interest in SSBs, since they can be applied in molecular biology techniques and analytical methods. Nanoarchaeum equitans, the only known representative of Archaea phylum Nanoarchaeota, is a hyperthermophilic, nanosized,...
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Novel primosomal protein B from Clostridium pastuerianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Novel primosomal protein B from Clostridium pasteurianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Conformation-family Monte Carlo: A new method for crystal structure prediction
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Plasma Amino Acids May Improve Prediction Accuracy of Cerebral Vasospasm after Aneurysmal Subarachnoid Haemorrhage
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A review on computer‐aided chemogenomics and drug repositioning for rational COVID ‐19 drug discovery
PublicationApplication of materials capable of energy harvesting to increase the efficiency and environmental adaptability is sometimes reflected in the ability of discovery of some traces in an environment―either experimentally or computationally―to enlarge practical application window. The emergence of computational methods, particularly computer-aided drug discovery (CADD), provides ample opportunities for the rapid discovery and development...