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Wyszukujesz frazę "protein structure modeling" wg kryterium: Temat

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    Wyświetlanie 1-5 z 5
    Tytuł:
    Unexpected domain composition of MACC1 links MET signaling and apoptosis
    Autorzy:
    Kokoszyńska, Katarzyna
    Kryński, Jacek
    Rychlewski, Leszek
    Wyrwicz, Lucjan
    Powiązania:
    https://bibliotekanauki.pl/articles/1040592.pdf
    Data publikacji:
    2009
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    protein structure modeling
    colorectal cancer
    bioinformatics
    death domain
    Opis:
    Colorectal cancer, one of the most challenging malignancies, still has a limited number of recognized prognostic and predictive markers indicating appropriate treatment. MACC1 (metastasis-associated in colon cancer-1), a novel regulator of tumor growth and metastasis has recently been identified as an important prognostic factor of metastatic disease in colorectal cancer. The mechanism of MACC1 activity remains undetermined. Here we apply a combination of fold recognition and homology modeling algorithms to draft MACC1 function. The applied methods revealed that the MACC1 protein consists of four domains: ZU5, SH3, and two C-terminal death domains (DD). Previously a similar domain architecture (ZU5-DD) was observed in other proteins, involved mainly in signal transduction and apoptosis regulation. Based on the specific aspects of the closest homologues' biology functional hypotheses on MACC1 are proposed. A broad range of bioinformatic analyzes indicates that MACC1, besides its involvement in signal transduction from the MET receptor, links MET signaling and apoptosis.
    Źródło:
    Acta Biochimica Polonica; 2009, 56, 2; 317-324
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    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:
    MOFOID - not only the protein modeling server.
    Autorzy:
    Szczesny, Pawel
    Wieczorek, Grzegorz
    Zielenkiewicz, Piotr
    Powiązania:
    https://bibliotekanauki.pl/articles/1041488.pdf
    Data publikacji:
    2005
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    protein structure prediction
    homology modeling
    Opis:
    MOFOID is a new server developed mainly for automated modeling of protein structures by their homology to the structures deposited in the PDB database. Selection of a template and calculation of the alignment is performed with the Smith-Waterman or Needleman-Wunsch algorithms implemented in the EMBOSS package. The final model is built and optimised with programs from the JACKAL package. The wide spectrum of options in the web-based interface and the possibility of uploading user's own alignment make MOFOID a suitable platform for testing new approaches in the alignment building. The server is available at https:// valis.ibb.waw.pl/mofoid/.
    Źródło:
    Acta Biochimica Polonica; 2005, 52, 1; 267-269
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Protein modeling and structure prediction with a reduced representation.
    Autorzy:
    Kolinski, Andrzej
    Powiązania:
    https://bibliotekanauki.pl/articles/1043267.pdf
    Data publikacji:
    2004
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    Monte Carlo simulations
    structure prediction
    comparative modeling
    lattice proteins
    protein folding
    Opis:
    Protein modeling could be done on various levels of structural details, from simplified lattice or continuous representations, through high resolution reduced models, employing the united atom representation, to all-atom models of the molecular mechanics. Here I describe a new high resolution reduced model, its force field and applications in the structural proteomics. The model uses a lattice representation with 800 possible orientations of the virtual alpha carbon-alpha carbon bonds. The sampling scheme of the conformational space employs the Replica Exchange Monte Carlo method. Knowledge-based potentials of the force field include: generic protein-like conformational biases, statistical potentials for the short-range conformational propensities, a model of the main chain hydrogen bonds and context-dependent statistical potentials describing the side group interactions. The model is more accurate than the previously designed lattice models and in many applications it is complementary and competitive in respect to the all-atom techniques. The test applications include: the ab initio structure prediction, multitemplate comparative modeling and structure prediction based on sparse experimental data. Especially, the new approach to comparative modeling could be a valuable tool of the structural proteomics. It is shown that the new approach goes beyond the range of applicability of the traditional methods of the protein comparative modeling.
    Źródło:
    Acta Biochimica Polonica; 2004, 51, 2; 349-371
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Implementation and evaluation of new protocol for comparative modeling of protein structures
    Autorzy:
    Strumillo, M.
    Dawid, A. E.
    Szczasiuk, A.
    Gront, D.
    Powiązania:
    https://bibliotekanauki.pl/articles/1935813.pdf
    Data publikacji:
    2014
    Wydawca:
    Politechnika Gdańska
    Tematy:
    protein structure prediction
    comparative modeling
    protein threading
    protein alignment
    BioShell
    Rosetta
    przewidywanie struktury białek
    modelowanie porównawcze
    gwintowania białka
    wyrównanie białka
    Opis:
    Template-based modeling (termed also Comparative or Homology Modeling) of a protein structure is one of ubiquitous tasks of structural bioinfor matics. The method can deliver model structures important for testing biological hypotheses, virtual docking and drug design. The performance of these methods is evaluated every two years during a Critical Assessment of Protein Structure Prediction (CASP) experiment. In this contribution we present a new automated protocol for template-base d modeling, which combines computational tools recently developed in our laboratory: the dat abase of protein domain structures (BDDB) with one dimensional and three dimensional thread ing applications. The protocol was tested during a CASP11 experiment.
    Źródło:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 4; 379--384
    1428-6394
    Pojawia się w:
    TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-5 z 5

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