Zobrazeno 1 - 10
of 153
pro vyhledávání: '"Bottaro, Sandro"'
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling tool to i
Externí odkaz:
http://arxiv.org/abs/1909.06780
Akademický článek
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Publikováno v:
Nucleic Acids Res. 46, 1674 (2018)
We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained representation of RNA designed for structure prediction and refinement. In our approach, the representation of a nucleotide consists of a point particle for the phosphate group and an
Externí odkaz:
http://arxiv.org/abs/1711.00741
Publikováno v:
Biochem. Biophys. Res. Commun. 498, 352 (2018)
Coarse-grained models can be of great help to address the problem of structure prediction in nucleic acids. On one hand they can make the prediction more efficient, while on the other hand, they can also help to identify the essential degrees of free
Externí odkaz:
http://arxiv.org/abs/1709.08691
Autor:
Kührová, Petra, Best, Robert B., Bottaro, Sandro, Bussi, Giovanni, Šponer, Jiří, Otyepka, Michal, Banáš, Pavel
Publikováno v:
J. Chem. Theory Comput. 2016, 12 (9), pp 4534-4548
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and RNA-protein interac
Externí odkaz:
http://arxiv.org/abs/1609.08276
Publikováno v:
J. Phys. Chem. Lett. 7, 4032 (2016)
We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using atomistic molecular dynamics simulations. We obtain a previously unreported estimation of the folding free energy using parallel tempering in combination with well-tem
Externí odkaz:
http://arxiv.org/abs/1609.07898
Publikováno v:
J. Chem. Theory Comput. 12, 2790 (2016)
The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement between simulations and experiments is not satisfactory due to inaccuracie
Externí odkaz:
http://arxiv.org/abs/1605.00934
Publikováno v:
Nucleic Acids Research 44, 5883 (2016)
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal structures are h
Externí odkaz:
http://arxiv.org/abs/1603.08952
Publikováno v:
Nucleic Acids Res. 43, 7260 (2015)
Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of RNAs is oft
Externí odkaz:
http://arxiv.org/abs/1506.09178
Publikováno v:
BMC Bioinformatics 2015, 16(Suppl 9):S6
Riboswitches are cis-acting regulatory RNA elements prevalently located in the leader sequences of bacterial mRNA. An adenine sensing riboswitch cis-regulates adeninosine deaminase gene (add) in Vibrio vulnificus. The structural mechanism regulating
Externí odkaz:
http://arxiv.org/abs/1504.07392