Wyniki wyszukiwania - BazTech

1

Backbone dihedral angles prediction servers for protein early-stage structure prediction

Smolarczyk Tomasz, Stapor Katarzyna, Roterman-Konieczna Irena

Bio-Algorithms and Med-Systems

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2019

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Vol. 15, no. 4

art. no. 20190034

EN

Three-dimensional protein structure prediction is an important task in science at the intersection of biology, chemistry, and informatics, and it is crucial for determining the protein function. In the two-stage protein folding model, based on an early- and late-stage intermediates, we propose to use state-of-the-art secondary structure prediction servers for backbone dihedral angles prediction and devise an early-stage structure. Early-stage structures are used as a starting point for protein folding simulations, and any errors in this stage affect the final predictions. We have shown that modern secondary structure prediction servers could increase the accuracy of early-stage predictions compared to previously reported models.

2

Modelling DNA and RNA secondary structures using matrix insertion-deletion systems

Kuppusamy L., Mahendran A.

International Journal of Applied Mathematics and Computer Science

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2016

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Vol. 26, no. 1

245--258

EN

Insertion and deletion are operations that occur commonly in DNA processing and RNA editing. Since biological macromolecules can be viewed as symbols, gene sequences can be represented as strings and structures can be interpreted as languages. This suggests that the bio-molecular structures that occur at different levels can be theoretically studied by formal languages. In the literature, there is no unique grammar formalism that captures various bio-molecular structures. To overcome this deficiency, in this paper, we introduce a simple grammar model called the matrix insertion–deletion system, and using it we model several bio-molecular structures that occur at the intramolecular, intermolecular and RNA secondary levels.

3

Dissimilar sequence: similar structure of proteins

Banach M., Konieczny L., Roterman I.

Bio-Algorithms and Med-Systems

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2016

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Vol. 12, no. 3

117--121

EN

Sequence-to-structure relation is one of the major objects of the analysis of protein folding problem. The pair of two small proteins (domains) of similar structure (β-hairpin/α-helix/β-hairpin) generated by the chains of similar length (about 60 amino acids) with very low sequence similarity (15%) is the object of the comparable analysis of 3D structure. The criterion for similarity estimation is the status of polypeptide chain with respect to the hydrophobic core structure. The fuzzy oil drop model is applied to reveal the differentiated status of fragments of the well-defined secondary structure. This analysis allows the interpretation of the structure in other than the geometric form as it is made based on secondary structure classification. The two compared highly similar proteins appear to be different with respect to the hydrophobic core structure.

4

Friction behavior of new composite bearing materials for printing machines and their special use under heavy operating conditions

Roik T., Gavrish A., Vitsiuk I., Khlus O.

Zeszyty Naukowe / Wyższa Szkoła Oficerska Wojsk Lądowych im. gen. T. Kościuszki

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2015

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Nr 4

100--108

EN

In the paper the friction film formation analysis of the new composite bearings based on powder nickel alloy EP975 with solid lubricant CaF2 powder after tribological tests has been presented. Dense films are formed during friction of contact surfaces for tribological tests at high speed (or temperature) and loads. Such films consist of chemical elements of friction pair and air oxygen. Friction film is a determining factor for the antifriction material. It is connected with the nature of friction films. The films can minimize friction and ensure stability of a friction unit. It depends on the combination of chemical elements and oxygen in the films formed. The chemical composition of friction films not only allows ex-plaining the mechanism of their formation, but also gives the possibility to forecast and control the functional properties of bearing materials in wide range of printing machines under operating conditions. New composite bearings can be successfully used in the military equipment nodes, such as sliding divices nodes of artillery weapons.

5

Przewidywanie struktury drugorzędowej białek metodą słownikową

Fabian P., Stąpor K.

Studia Informatica

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2014

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Vol. 35, nr 1

57--68

EN

This paper describes a method of predicting the secondary structure of proteins, based on dictionaries of subsequences. These subsequences are derived from records available in the PDB database. Depending on the construction of the learning set, accuracies of up to 79% have been achieved. Dictionaries use hashing functions, which make them fast and capable of storing large sets of substrings.

PL

W artykule opisano sposób przewidywania struktury drugorzędowej białek, oparty na słownikach podciągów. Sekwencje te są pobierane z danych dostępnych w bazie danych PDB. W zależności od konstrukcji zestawu uczącego, osiągnięto dokładność do 79%. Do szybkiego dostępu do słowników zawierających dużą liczbę podciągów zastosowano funkcje mieszające.

6

SSTMProt, a point mutation sensitive tool to combine results and to predict the consensus sequence, and secondary structure of transmembrane proteins

Jastrzębski J. P.

Bio-Algorithms and Med-Systems

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2011

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Vol. 7, no. 4

67--78

EN

The efficiency of predictions of protein secondary structures can be increased by treating this process as a cycle of steps, where each step is an approach to the single natural event in folding process (model and simulation of successive events). The set of simulation steps qualifies reliability of in silico simulation of single steps, allowing to verify the correctness of each step as well as to retain sensitivity in case of a single amino acidic substitution. For this purpose the three-part algorithm (SSTMProt) has been designed. This algorithm combines the results of known methods of prediction of proteins secondary structure. Furthermore, the efficiency of this algorithm has been verified using the models received from the RCSB PDB (the Research Collaboratory for Structural Bioinformatics – Protein Data Base; http://www.rcsb.org). The accuracy of known methods has been compared with the accuracy of designed algorithms. The accuracy has been tested by the comparison of true secondary structure with predicted secondary structure of a given protein. The results of accuracy test has been presented as percentage values of similarity between both secondary structures: predicted structure using known method vs. true structure and predicted structure using designed method vs. true structure. The results demonstrate 20-30% higher accuracy of prediction for designed algorithms then for adequate known methods. The test of sensitivity has been done for proteins of a very conservative and stable structure (subunits of bovine cytochrome c oxidase and bacterial ATP-ase, bovine rhodopsin and human hemoblobin as a globular but alpha-helical protein). The influence of a single amino acid substitution on a resulted secondary structure predicted by SSTMProt algorithms has been examined. The repeatability of elaborated algorithms is 100% and each of all 12 tested combinations of methods were sensitive on a single amino acid substitution. All tests have been done for 10 models of native forms of proteins of known structure (models downloaded from the RCSB PDB 1HBB, 1HBS, 1OCC, 1U17, 1C17) and over 500 modified models; 30 known methods of prediction of secondary structure of proteins and 40 combinations of these methods included in three versions of elaborated algorithms have been examined for each protein model.

7

Język zapytań dla molekularnych struktur białkowych

Wieczorek D., Małysiak-Mrozek B., Mrozek D.

Studia Informatica

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2010

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Vol. 31, nr 2A

267-287

PL

Reprezentacja białek w postaci struktury drugorzędowej dostarcza ważnych informacji dotyczących budowy białek i jest często wykorzystywana w procesie poszukiwania podobieństwa białek. Ponieważ istniejące komercyjne systemy zarządzania bazami danych nie udostępniają zintegrowanych sposobów zaawansowanego przetwarzania danych biologicznych na poziomie języka SQL, proces poszukiwania podobieństwa strukturalnego jest zwykle realizowany przez narzędzia zewnętrzne. W niniejszym artykule przedstawiono opracowany i zaimplementowany przez autorów język PSS-SQL, pozwalający na poszukiwanie w bazie danych białek o strukturze drugorzędowej podobnej do struktury wyspecyfikowanej przez użytkownika. W ten sposób otrzymujemy łatwy w zapisie, deklaratywny język do poszukiwania podobieństwa strukturalnego białek.

EN

Secondary structure representation of proteins provides important information regarding protein general construction and shape. This representation is often used in protein similarity searching. Since existing commercial database management systems do not offer integrated exploration methods for biological data e.g. at the level of the SQL language, the structural similarity searching is usually performed by external tools. In the paper, we present our newly developed PSS-SQL language, which allows searching the database in order to identify proteins having secondary structure similar to the structure specified by the user in a PSS-SQL query. Therefore, we provide a simple and declarative language for protein structure similarity searching.

8

A method for matching sequences of protein secondary structures

Wieczorek D., Małysiak-Mrozek B., Kozielski S., Mrozek D.

Journal of Medical Informatics & Technologies

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2010

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Vol. 16

133--137

EN

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.

9

A declarative query language for protein secondary structures

Wieczorek D., Małysiak-Mrozek B., Kozielski S., Mrozek D.

Journal of Medical Informatics & Technologies

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2010

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Vol. 16

139--148

EN

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.

10

Structural properties of proteolytic-accessible bioactive fragments of selected animal proteins

Dziuba J., Niklewicz M., Iwaniak A., Darewicz M., Minkiewicz P.

Polimery

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2005

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T. 50, nr 6

424-428

EN

The computer simulation of the distribution of biologically active fragments and bonds which are predicted to be susceptible to the action of endopeptidases of known specificity, hydropathy index and prediction of secondary structures were performed. The average values of hydropathy index calculated for bioactive fragments of selected animal proteins predicted in silico to be released by proteolytic enzymes as well as surroundings of such fragments show that they are hydrophilic. The most frequently occurring structure in the animal proteins bioactive fragments with surroundings is b-strand. There is no preferable secondary structure in the bioactive fragments encrypted in the animal protein sequences. Our findings suggest that the distribution of bioactive fragments may favour their release by proteinases.

PL

Przedstawiono wyniki komputerowej symulacji rozmieszczenia biologicznie aktywnych fragmentów oraz wiązań peptydowych podatnych na działanie endopeptyzad o określonej specyficzności, przewidywania zawartości struktur drugorzędowych oraz indeksu hydropatii. Najczęściej występującym motywem strukturalnym wśród bioaktywnych peptydów wraz z otoczeniem jest struktura b-harmonijkowa. Nie stwierdzono dominującego udziału żadnej ze struktur drugorzędowych w bioaktywnych peptydach występujących w sekwencjach badanych białek zwierzęcych. Średnie wartości indeksu hydropatii wskazują, że zarówno bioaktywne fragmenty uwolnione in silico z sekwencji wybranych białek zwierzęcych przez enzymy proteolityczne, jak i ich otoczenie są hydrofilowe. Wyniki badań sugerują, że rozmieszczenie bioaktywnych peptydów sprzyja ich uwalnianiu przez enzymy proteolityczne.

11

Wpływ zawartości aluminium i prędkości chłodzenia na strukturę i właściwości stopów na osnowie fazy międzymetalicznej TiAl

Szkliniarz W., Mikuszewski T., Juszczyk B.

Rudy i Metale Nieżelazne

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2004

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R. 49, nr 4

196-201

PL

Opierając się na danych literaturowych oraz wynikach własnych badań dokonano oceny wpływu zawartości aluminium i parametrów obróbki cieplnej na strukturę pierwotną i wtórną oraz wybrane właściwości dwufazowych stopów na osnowie fazy międzymetalicznej TiAl. Zbadano wpływ prędkości chłodzenia po wyżarzaniu na morfologię płytkową wybranego stopu. Określono wzajemne zależności pomiędzy zawartością aluminium w stopach, odległościami międzypłytkowymi faz tworzących płytkowe kolonie oraz twardością stopów.

EN

Based on the literature data and results of author's own investigations, assessment of an effect of aluminium content and heat treatment parameters on the primary and secondary structure and selected properties of the TiAl intermetallic phase based two-phase alloys has been presented. An effect of a cooling rate after annealing on the lamellar morphology of selected alloy was investigated. Interdependence between aluminium content in the alloys, inter-lamellar spacing between lamellar phase colonies and an alloy hardness has been determined.