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Wyświetlanie 1-15 z 55
Tytuł:
A declarative query language for protein secondary structures
Autorzy:
Wieczorek, D.
Małysiak-Mrozek, B.
Kozielski, S.
Mrozek, D.
Powiązania:
https://bibliotekanauki.pl/articles/333087.pdf
Data publikacji:
2010
Wydawca:
Uniwersytet Śląski. Wydział Informatyki i Nauki o Materiałach. Instytut Informatyki. Zakład Systemów Komputerowych
Tematy:
proteiny
struktura drugorzędowa
podobieństwa białek
język zapytań
proteins
secondary structure
protein similarity
query language
Opis:
Searching proteins on their secondary structures provides a rough and fast method of identification of molecules having a similar fold. Since existing database management systems do not offer integrated exploration methods for querying protein structures, the structural similarity searching is usually performed by external tools. This often lengthens the processing time and requires additional processing steps, like adaptation of input and output data formats. In the paper, we present the extended SQL language, which allows searching a database in order to find proteins having secondary structures similar to the structural pattern specified by a user. Presented query language is integrated with the relational database management system and it simplifies the manipulation of biological data.
Źródło:
Journal of Medical Informatics & Technologies; 2010, 16; 139-148
1642-6037
Pojawia się w:
Journal of Medical Informatics & Technologies
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A method for matching sequences of protein secondary structures
Autorzy:
Wieczorek, D.
Małysiak-Mrozek, B.
Kozielski, S.
Mrozek, D.
Powiązania:
https://bibliotekanauki.pl/articles/333075.pdf
Data publikacji:
2010
Wydawca:
Uniwersytet Śląski. Wydział Informatyki i Nauki o Materiałach. Instytut Informatyki. Zakład Systemów Komputerowych
Tematy:
proteiny
struktura drugorzędowa
podobieństwa białek
wyrównanie
proteins
secondary structure
protein similarity
alignment
Opis:
Alignment of specific regions of two biological molecules is a basic method for determination how similar these two molecules are. There are several methods of optimal alignment that were developed through many years. However, they are dedicated for nucleotide sequences of DNA⁄RNA or amino acid sequences of proteins. Since the construction of proteins can also be analyzed at the level of secondary structure (and higher), we need a comparative method, which would allow us to determine the similarity between biological particles at this level and express it through the appropriate similarity measure. For this reason, we have modified an existing Smith–Waterman method towards matching sequences of secondary structures elements (SSEs). In the paper, we present our modification to the method. We also describe how we find several alternative and equally optimal alignment paths on the basis of the characteristics of compared sequences. Presented alignment method is used in the PSS–SQL language, which allows searching a database in order to find proteins having secondary structures similar to the structural pattern specified by a user.
Źródło:
Journal of Medical Informatics & Technologies; 2010, 16; 133-137
1642-6037
Pojawia się w:
Journal of Medical Informatics & Technologies
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A new approach to homology modeling
Autorzy:
He, Y.
Scheraga, H. A.
Rackovsky, S.
Powiązania:
https://bibliotekanauki.pl/articles/1954429.pdf
Data publikacji:
2022-02-01
Wydawca:
Politechnika Gdańska
Tematy:
protein structure prediction
physical properties
Kidera factors
Fourier transformation
coarse-grained force field
Opis:
The need to interpret experimental results led to, first, an all-atom force field, followed by a coarse-grained one. As an aid to these force fields, a new approach is introduced here to predict protein structure based on the physical properties of th e amino acids. This approach includes three key components: Kidera factors describing the physical properties, Fourier transformation and UNRES coarse-grained force field simulations. Different from traditional homology modeling methods which are based on evolution, this approach is physics-based, and does not have the same weaknesses as the traditional homology modeling methods. Our results show that this approach can produce above average prediction results, and can be used as a useful tool for protein structure prediction.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 3; 211--218
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A short review on proteomics and its applications
Autorzy:
Chandrasekhar, K.
Dileep, A.
Lebonah, D.E.
Pramoda Kumari, J.
Powiązania:
https://bibliotekanauki.pl/articles/11309.pdf
Data publikacji:
2014
Wydawca:
Przedsiębiorstwo Wydawnictw Naukowych Darwin / Scientific Publishing House DARWIN
Tematy:
proteomics
application
protein function
protein structure
stress condition
metabolism
2-D electrophoresis
disease treatment
novel protein
Opis:
Proteomics is the large scale of study of proteins, particularly their function and structure. Proteomics is an excellent approach for studying changes in metabolism in response to different stress conditions. In the present review focused on different types of techniques for the analysis of expressed proteins. The techniques includes 2-D gel electrophoresis, MALDI-TOF/MS etc., play a vital role for the analysis of novel proteins and their role in disease maintenance and treatment. The review also concentrated on applicative perspective of proteomics in the fields of biomedical, agriculture and food.
Źródło:
International Letters of Natural Sciences; 2014, 12, 1
2300-9675
Pojawia się w:
International Letters of Natural Sciences
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Aminokwasy, glikany, peptydy i białka w ścieżkach diagnostycznych i terapeutycznych chorób cywilizacyjnych XXI wieku : projektowanie i charakterystyka fizykochemiczna oraz strukturalna
Amino acids, glycans, peptides and proteins in the diagnostic and therapeutic pathways of the 21st century civilization diseases : design, physicochemical and structural characterisation
Autorzy:
Bylińska, Irena
Dzierżyńska, Maria
Giżyńska, Małgorzata
Guzow, Katarzyna
Jankowska, Elżbieta
Jurczak, Przemysław
Kaczyński, Zbigniew
Karska, Natalia
Kowalczyk, Agnieszka
Kuncewicz, Katarzyna
Orlikowska, Marta
Sawicka, Justyna
Spodzieja, Marta
Szpakowska, Nikola
Szymańska, Aneta
Wieczerzak, Ewa
Witkowska, Julia
Rodziewicz-Motowidło, Sylwia
Powiązania:
https://bibliotekanauki.pl/articles/2200549.pdf
Data publikacji:
2022
Wydawca:
Polskie Towarzystwo Chemiczne
Tematy:
fluorophores
fluorescence spectroscopy
antimicrobial activity
anticancer activity
Cystapep
Stahylococcus aureus
antimicrobial compounds
amyloidogenic protein
mutagenesis
fibrilization
proteasome
aging
neurodegeneration
self-assembling peptides
tissue engineering
biomaterials
immune checkpoints
peptide inhibitors
immunotherapy
ligands of TAP protein
viral diseases
NMR structure of the UL49.5 protein
glycans
glycoconjugates
fluorofory
spektroskopia fluorescencyjna
aktywność przeciwdrobnoustrojowa
aktywność antynowotworowa
Staphylococcus aureus
związki przeciwbakteryjne
białko amyloidogenne
mutageneza
fibrylizacja
proteasom
procesy starzeniowe
neurodegeneracja
peptydy samoorganizujące
inżynieria tkankowa
biomateriały
punkty kontrolne układu immunologicznego
inhibitory peptydowe
immunoterapia
ligandy białka TAP
choroby wirusowe,
struktura NMR białka UL49.5
glikany
glikokoniugaty
Opis:
The civilization diseases of the 21st century are non-infectious disorders, affecting a large part of modern society. They are associated with the significant development of industry and technology, and hence with environmental pollution and an unhealthy lifestyle. These factors have led to the development of many civilization diseases, which currently include: cardiovascular diseases, respiratory diseases, diabetes, obesity, malignant tumors, gastrointestinal diseases, mental disorders and allergic diseases. The development of technologies, including modern therapies and new drugs, resulted in increase in life expectancy. This creates a global problem of an aging population with an increasing number of diseases of the old age, i.e. dementias. In addition, sedentary lifestyles and changing diets are the reasons why more and more people develop metabolic diseases, as well as neurological and cognitive disorders characterized by progressive damage to nerve cells and dementia. Currently, problem on a global scale is also the growing resistance to existing antimicrobial drugs. Therefore, the scientists face many challenges related to searching for the causes of these diseases, their diagnosis and treatment. Scientific research conducted at the Department of Biomedical Chemistry at the Faculty of Chemistry of the University of Gdańsk is part of this research trend. In this publication, we discuss various research topics with the long-term aim of solving the problems associated with the diseases mentioned above. The following chapters are dedicated to (i) looking for new effective fluorophores with diagnostic and anti-cancer activity; (ii) designing of new compounds with antibacterial and antiviral activity and their synthesis; (iii) investigating the mechanisms of amyloid deposit formation by human cystatin C and possibilities of inhibition of this process; (iv) designing and studies of compounds activating the proteasome with the potential to suppress the development of neurodegenerative diseases; (v) designing peptide fibrils and hydrogels as drug carriers; (vi) searching for peptide inhibitors of immune checkpoint as potential drugs for immunotherapy; (vii) studying the mechanism of action of selected herpesviruses by determining the structure of viral proteins and (viii) studying the composition of natural glycans and glycoconjugates in order to better understand the mechanisms of interaction of bacteria with the environment or with the host.
Źródło:
Wiadomości Chemiczne; 2022, 76, 5-6; 393--431
0043-5104
2300-0295
Pojawia się w:
Wiadomości Chemiczne
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
An example of template based protein structure modeling by global optimization
Autorzy:
Joo, K.
Joung, I.
Lee, J.
Powiązania:
https://bibliotekanauki.pl/articles/1938628.pdf
Data publikacji:
2016
Wydawca:
Politechnika Gdańska
Tematy:
template based modeling
protein structure modeling
global optimization
casp
homology modeling
sequence alignment
fold recognition
Opis:
CASP (Critical Assessment of protein Structure Prediction) is a community-wide experiment for protein structure prediction taking place every two years since 1994. In CASP 11 held in 2014, according to the official CASP 11 assessment, our method named `nns' was ranked as the second best server method based on models ranked as first out of 81 targets. In `nns', we applied the powerful global optimization method of conformational space annealing to three stages of optimization, including multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain remodeling. For the fold recognition, a new alignment method called CRF align was used. The good performance of the nns server method is attributed to the successful fold recognition carried out by combined methods including CRF align, and the current modeling formulation incorporating accurate structural aspects collected from multiple templates. In this article, we provide a successful example of `nns' predictions for T0776, for which all details of intermediate modeling data are provided.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2016, 20, 4; 341-352
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Analiza wplywu cech odmianowych pszenicy i stopnia wyciagu maki na wyniki oznaczen metoda Durotest
Autorzy:
Makowska, A
Strybe, K.
Obuchowski, W.
Powiązania:
https://bibliotekanauki.pl/articles/826181.pdf
Data publikacji:
2000
Wydawca:
Polskie Towarzystwo Technologów Żywności
Tematy:
struktura bialek
metoda Durotest
pszenica twarda
makarony
cechy odmianowe
friabilina
oznaczanie
zawartosc bialka
maka pszenna
pszenica
pszenica zwyczajna
protein structure
Durotest method
durum wheat
pasta
cultivar trait
friabilin
determination
protein content
wheat flour
wheat
common wheat
Opis:
Badano wpływ wyciągu mąki, jej rozdrobnienia i odmiany z jakiej pochodzi, na wyniki oznaczeń zawartości mąki z pszenicy vulgare w surowcu makaronowym. Analizie poddano 11 krajowych odmian pszenicy zwyczajnej, 2 handlowych partii pszenicy durum i 6 mąk i kaszek pochodzących z przemiału jednej partii pszenicy durum. Przeprowadzona analiza statystyczna wyników wykazała istotne różnice pomiędzy mąką całoziamową, a mąką o wyciągu 65%, a także pomiędzy ziarnem krajowych odmian pszenicy zwyczajnej. Nie wykazano natomiast wpływu rozdrobnienia surowca na wyniki „Durotestu”. Mimo to wielokrotnie większe różnice w zawartości friabiliny, jakie występują pomiędzy pszenicą gatunku durum i vulgare powodują, że test ten jest przydatny także do określania stopnia zanieczyszczenia semoliny mąką z pszenicy zwyczajnej w szerokim spektrum wyciągu.
The effect of extraction yield, avarage particle size of flour, and wheat cultivar used on the results of durotest were evaluated. The experiments were carried out on 11 domestic wheat cultivars, two commercial durum samples and 6 semolina streams obtained from different millstreams of durum wheat. It was found statistically significant difference durotest results between whole and white flour. It was found also, that different cultivars of domestic vulgare wheat show different amount of friabilin. Nevertheless, differcces in friabilin content between durum and vulgare products were much higher, and test could be used also to evaluate non-durum flours in semolina products.
Źródło:
Żywność Nauka Technologia Jakość; 2000, 07, 3; 48-57
1425-6959
Pojawia się w:
Żywność Nauka Technologia Jakość
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Ancient history of X-ray crystal structure of B-DNA oligomers and its perspective
Autorzy:
Grzeskowiak, K.
Ohishi, H.
Powiązania:
https://bibliotekanauki.pl/articles/80367.pdf
Data publikacji:
2011
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
ancient history
X-ray crystallography
crystal structure
DNA oligomer
DNA binding protein
DNA binding drug
nanotechnology
methylation
nanotube
antitumour agent
DNA restriction
DNA sequence
protein
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2011, 92, 3
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Attaching a spin to a protein - site-directed spin labeling in structural biology
Autorzy:
Czogalla, Aleksander
Pieciul, Aldona
Jezierski, Adam
Sikorski, Aleksander
Powiązania:
https://bibliotekanauki.pl/articles/1041067.pdf
Data publikacji:
2007
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
protein structure
site-directed spin labeling
electron paramagnetic resonance (EPR) spectroscopy
Opis:
Site-directed spin labeling and electron paramagnetic resonance spectroscopy have recently experienced an outburst of multiple applications in protein science. Numerous interesting strategies have been introduced for determining the structure of proteins and its conformational changes at the level of the backbone fold. Moreover, considerable technical development in the field makes the technique an attractive approach for the study of structure and dynamics of membrane proteins and large biological complexes at physiological conditions. This review focuses on a brief description of site-directed spin labeling-derived techniques in the context of their recent applications.
Źródło:
Acta Biochimica Polonica; 2007, 54, 2; 235-244
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Changes of albumin secondary structure after palmitic acid binding : FT-IR spectroscopic study
Autorzy:
Oleszko, A
Hartwich, J.
Gąsior-Głogowska, M.
Olsztyńska-Janus, S.
Powiązania:
https://bibliotekanauki.pl/articles/307332.pdf
Data publikacji:
2018
Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Tematy:
kwas palmitynowy
albumina
spektrometria FTIR
palmitic acid
albumin
Fourier transform infrared spectroscopy
protein secondary structure
Opis:
Purpose: Albumin is an universal transport protein. Plasma pool of free fatty acids arising from triglyceride hydrolysis, critical in energy metabolism and etiology of metabolic disorders is transported by albumin. According to various studies albumin has from seven to nine binding sites with diverse affinity to long chain fatty acids. X-ray diffraction crystallography measurements have provided data only for pure human serum albumin or albumin with fully saturated binding sites. These results have shown that amount of -helices is higher after fatty acids binding. Molecular mechanics simulations suggest that binding of fatty acids in two high-affinity sites leads to major conformational changes in albumin structure. The aim of this research was to investigate albumin secondary structure upon gradually increasing fatty acids to protein mole ratio. Methods: Fourier transform infrared spectroscopy was applied to study changes of bovine serum albumin (as an analogue of human serum albumin) -helical structures after binding palmitic acid in a range of 0–20 palmitic acid: albumin molar ratios representing pure protein, partial, full saturation and excess binding sites capacity. Results: Amount of -helices was increasing along with the amount of palmitic acid: bovine serum albumin molar ratio and reached maximum value around 2 mol/mol. Conclusions: Our studies confirmed molecular mechanics simulations and crystallographic studies. Palmitic acid binding in two high-affinity sites leads to major structural changes, filling another sites only slightly influenced bovine serum albumin secondary structure. The systematic study of fatty acids and albumin interactions, using an experimental model mimicking metabolic disorders, may results in new tools for personalized nanopharmacotherapy.
Źródło:
Acta of Bioengineering and Biomechanics; 2018, 20, 1; 59-64
1509-409X
2450-6303
Pojawia się w:
Acta of Bioengineering and Biomechanics
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Cloning of the Haemophilus influenzae Dam methyltransferase and analysis of its relationship to the Dam methyltransferase encoded by the HP1 phage.
Autorzy:
Bujnicki, Janusz
Radlińska, Monika
Zaleski, Piotr
Piekarowicz, Andrzej
Powiązania:
https://bibliotekanauki.pl/articles/1044039.pdf
Data publikacji:
2001
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
protein structure
sequence specificity
DNA methyltransferase
bioinformatics
molecular evolution
Opis:
In this paper we report cloning and experimental characterization of the DNA adenine methyltransferase (dam) gene from Haemophilus influenzae and comparison of ts product with the Dam protein from the lysogenic phage of H. influenzae, HP1. Molecular modeling of M.HinDam and M.HP1Dam was carried out, providing a framework for a comparative analysis of these enzymes and their close homologs in the tructural context. Both proteins share the common fold and essential cofactor-bind ng and catalytic residues despite overall divergence. However, subtle but significant differences in the cofactor-binding pocket have been identified. Moreover, while M.HinDam seems to contact its target DNA sequence using a number of loops, most of them are missing from M.HP1Dam. Analysis of both MTases suggests that their catalytic activity was derived from a common ancestor, but similar sequence specificities rose by convergence.
Źródło:
Acta Biochimica Polonica; 2001, 48, 4; 969-983
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Collagens, the basic proteins of the human body
Autorzy:
Czarny-Ratajczak, M
Latos-Bielenska, A.
Powiązania:
https://bibliotekanauki.pl/articles/2042040.pdf
Data publikacji:
2000
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
human disease
human body
collagen gene
fibrillar collagen
classification
structure
non-fibrillar collagen
protein
mutation
collagen
Źródło:
Journal of Applied Genetics; 2000, 41, 4; 317-330
1234-1983
Pojawia się w:
Journal of Applied Genetics
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Comparison of proteins based on segments structural similarity.
Autorzy:
Plewczynski, Dariusz
Pas, Jakub
von Grotthuss, Marcin
Rychlewski, Leszek
Powiązania:
https://bibliotekanauki.pl/articles/1043336.pdf
Data publikacji:
2004
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
3D-hit
protein structure comparison
liveBench
protein structure
toolShop
structural hashing
Opis:
We present here a simple method for fast and accurate comparison of proteins using their structures. The algorithm is based on structural alignment of segments of Ca chains (with size of 99 or 199 residues). The method is optimized in terms of speed and accuracy. We test it on 97 representative proteins with the similarity measure based on the SCOP classification. We compare our algorithm with the LGscore2 automatic method. Our method has the same accuracy as the LGscore2 algorithm with much faster processing of the whole test set, which is promising. A second test is done using the ToolShop structure prediction evaluation program and shows that our tool is on average slightly less sensitive than the DALI server. Both algorithms give a similar number of correct models, however, the final alignment quality is better in the case of DALI. Our method was implemented under the name 3D-Hit as a web server at http://3dhit.bioinfo.pl/ free for academic use, with a weekly updated database containing a set of 5000 structures from the Protein Data Bank with non-homologous sequences.
Źródło:
Acta Biochimica Polonica; 2004, 51, 1; 161-172
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Computer simulations of protein folding with a small number of distance restraints.
Autorzy:
Sikorski, Andrzej
Kolinski, Andrzej
Skolnick, Jeffrey
Powiązania:
https://bibliotekanauki.pl/articles/1043733.pdf
Data publikacji:
2002
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
lattice models
NMR structure refinement
Monte Carlo method
reduced protein models
protein folding
Opis:
A high coordination lattice model was used to represent the protein chain. Lattice points correspond to amino-acid side groups. A complicated force field was designed in order to reproduce a protein-like behavior of the chain. Long-distance tertiary restraints were also introduced into the model. The Replica Exchange Monte Carlo method was applied to find the lowest energy states of the folded chain and to solve the problem of multiple minima. In this method, a set of replicas of the model chain was simulated independently in different temperatures with the exchanges of replicas allowed. The model chains, which consisted of up to 100 residues, were folded to structures whose root-mean-square deviation (RMSD) from their native state was between 2.5 and 5 Å. Introduction of restrain based on the positions of the backbone hydrogen atoms led to an improvement in the number of successful simulation runs. A small improvement (about 0.5 Å) was also achieved in the RMSD of the folds. The proposed method can be used for the refinement of structures determined experimentally from NMR data.
Źródło:
Acta Biochimica Polonica; 2002, 49, 3; 683-692
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Correlated mutations in selected protein families
Autorzy:
Leluk, J.
Sobczyk, M.
Becella, Ł.
Powiązania:
https://bibliotekanauki.pl/articles/1986920.pdf
Data publikacji:
2002
Wydawca:
Politechnika Gdańska
Tematy:
protein sequence
multiple alignment
tertiary structure
mutational correlation
genetic semihomology algorithm
Opis:
Four different protein families (two proteinase inhibitor families, myoglobins and lysozymes) were surveyed for correlated mutations with respect to the position distance and their significance in structure stabilization and biological activity. They were chosen for this study in order to verify the currently admitted model of mutational correlation relationship with respect to spatial contact of the residues and contribution in protein biological activity. There was observed high contribution of spatially dispersed residues (which are also not involved in the protein active center) in mutational correlation. Because of the significantly large distance between correlated positions these cases do not correspond explicitly to any mechanism included in current hypotheses. It is suggested that the role of residue spatial contact in structure preservation, intermolecular interaction and active site rescue mechanisms only partially explains the correlation phenomenon.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2002, 6, 3; 469-482
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
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