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    Wyświetlanie 1-4 z 4
    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 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:
    Electrostatics in computer-aided drug design
    Autorzy:
    Naray-Szabo, G.
    Matyus, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/1953955.pdf
    Data publikacji:
    1998
    Wydawca:
    Politechnika Gdańska
    Tematy:
    electrostatics
    drug design
    molecular electrostatic potential
    molecular electrostatic field
    similarity
    pharmacophore
    ComFa method
    protein-ligand interaction
    Opis:
    Hydrogen bonds and charge-charge interactions, determined by molecular electrostatics, play essential role in biopolymer-ligand associations. Accordingly, electrostatics is crucial in the qualitative and quantitative characterisation of the binding of drugs to their target molecules. In the following, we will give an account on the role of molecular electrostatics in a drug design, laying emphasis on our own work. We will survey the most important computation methods of molecular electrostatic potentials, then outline basic aspects of molecular recognition: steric, electrostatic and hydrophobic complementarity. On the basis of the complementarity, we will also define molecular similarity and discuss various applications of these concepts to the treatment of protein-ligand interactions and a rational drug design. Special attention will be paid to a receptor mapping and to a comparative molecular field analysis, with some our recent applications. A further important point will be the molecular electrostatic field (potential gradient) as a hydrophobicity measure. We will argue that the hydrophobic complementarity and similarity can be treated on the basis of matching regions of the interacting molecules that are characterised by a similar magnitude of the electrostatic field. The concept of the electrostatic complementarity will be extended to enzyme-substrate interactions, providing a firm basis for the quantitative estimation of catalytic rate enhancement.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 1998, 2, 4; 551-562
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Beyond sequence similarity – the curious case of GW/WG protein domain
    Autorzy:
    Karlowski, W.M.
    Powiązania:
    https://bibliotekanauki.pl/articles/79861.pdf
    Data publikacji:
    2011
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    RNA silencing
    gene expression
    protein domain
    amino acid sequence
    Arabidopsis thaliana
    Vitis vinifera
    cysteine
    phenylalanine
    histidine
    methionine
    tyrosine
    sequence similarity
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2011, 92, 4
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-4 z 4

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