Temat: coarse-grained modeling - Katalog OPAC zbiorów

Skocz do pozycji: 1.

Tytuł:: Mechanical unfolding of DDFLN4 studied by coarse-grained knowledge-based CABS model
Autorzy:: Kouza, M.
Jamroz, M.
Gront, D.
Kmiecik, S.
Koliński, A.
Powiązania:: https://bibliotekanauki.pl/articles/1935814.pdf
Data publikacji:: 2014
Wydawca:: Politechnika Gdańska
Tematy:: CABS
coarse-grained modeling
lattice model
mechanical unfolding of proteins
Opis:: Mechanical unfolding of the fourth domain of Distyostelium discoideum filamin ( DDFLN 4) was studied using a CABS – coarse-grained knowledge-based protein model. Our study demonstrates that CABS is capable of reproducing the unfolding free energy landscape of protein unfolding and highlights an important role of non-native interactions in the protein unfolding process. The obtained three peaks in the force-extension profile suggest a four-state picture of DDFLN 4 protein unfolding and correspond reasonably to the results of the all-atom simulation in explicit solvent.
Źródło:: TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 4; 373--378
1428-6394
Pojawia się w:: TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:: Biblioteka Nauki

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Skocz do pozycji: 2.

Tytuł:: Coarse-grained modeling of protein structure, dynamics and protein-protein interactions
Autorzy:: Koliński, A.
Kmiecik, S.
Jamróz, M.
Błaszczyk, M.
Kouza, M.
Kurciński, M.
Powiązania:: https://bibliotekanauki.pl/articles/1954428.pdf
Data publikacji:: 2014
Wydawca:: Politechnika Gdańska
Tematy:: coarse-grained modeling
protein folding
protein dynamics
molecular docking
protein docking
Opis:: Theoretical prediction of protein structures and dynamics is essential for understanding the molecular basis of drug action, metabolic and signaling pathways in living cells, designing new technologies in the life science and material sciences . We developed and validated a novel multiscale methodology for the study of protein folding processes including flexible docking of proteins and peptides. The new modeling technique starts from coarse-grained large-scale simulations, followed by selection of the most plausible final structures and intermediates and, finally, by an all-atom rectification of the obtained structures. Except for the most basic bioinformatics tools, the entire computational methodology is based on the models and algorithms developed in our lab. The coarse-grained simulations are based on a high-resolution lattice representation of protein structures, a knowledge based statistical force field and efficient Monte Carlo dynamics schemes, including Replica Exchange algorithms. This paper focuses on the description of the coarse-grained CABS model and its selected applications.
Źródło:: TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 3; 219--229
1428-6394
Pojawia się w:: TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:: Biblioteka Nauki

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