Zobrazeno 1 - 10
of 44
pro vyhledávání: '"A. Pérez de Alba Ortíz"'
Autor:
Bedolla-Montiel, Edwin A., Lange, Jochem T., Pérez de Alba Ortíz, Alberto, Dijkstra, Marjolein
Publikováno v:
Journal of Chemical Physics; 6/28/2024, Vol. 160 Issue 24, p1-12, 12p
Publikováno v:
PLoS Computational Biology, Vol 18, Iss 5, p e1010113 (2022)
Hoogsteen (HG) base pairing is characterized by a 180° rotation of the purine base with respect to the Watson-Crick-Franklin (WCF) motif. Recently, it has been found that both conformations coexist in a dynamical equilibrium and that several biologi
Externí odkaz:
https://doaj.org/article/a2b60f9c0a1b4185a68e2fad9e2a74f1
Autor:
Pérez de Alba Ortíz, Alberto1,2 (AUTHOR), Vreede, Jocelyne1 (AUTHOR), Ensing, Bernd1,3 (AUTHOR) b.ensing@uva.nl
Publikováno v:
PLoS Computational Biology. 5/26/2022, Vol. 18 Issue 5, p1-15. 15p. 1 Diagram, 2 Graphs.
Autor:
Alberto Pérez de Alba Ortíz, Oleksandr O. Sofronov, Huib J. Bakker, Giulia Giubertoni, Bernd Ensing
Publikováno v:
The Journal of Physical Chemistry Letters
Journal of Physical Chemistry Letters, 11(9), 3466-3472. American Chemical Society
Journal of Physical Chemistry Letters, 11(9), 3466-3472. American Chemical Society
The carboxyl (COOH) side chain groups of amino acids, such as aspartic acid, play an important role in biochemical processes, including enzymatic proton transport. In many theoretical studies, it was found that the (bio)chemical reactivity of the car
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6a9ad596b19217f90136e2c61b8aade5
https://doi.org/10.1021/acs.jpclett.0c00711
https://doi.org/10.1021/acs.jpclett.0c00711
Publikováno v:
Nucleic Acids Research, 47(21), 11069-11076. Oxford University Press
Nucleic Acids Research
Nucleic Acids Research
DNA predominantly contains Watson–Crick (WC) base pairs, but a non-negligible fraction of base pairs are in the Hoogsteen (HG) hydrogen bonding motif at any time. In HG, the purine is rotated ∼180° relative to the WC motif. The transitions betwe
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6a2e8fd28d36a6ff63b33b15d984b1a8
https://doi.org/10.1093/nar/gkz837
https://doi.org/10.1093/nar/gkz837
Publikováno v:
Journal of Chemical Physics; 8/21/2018, Vol. 149 Issue 7, pN.PAG-N.PAG, 13p, 4 Diagrams, 12 Graphs
Discovering Collective Variables of Molecular Transitions via Genetic Algorithms and Neural Networks
Publikováno v:
Journal of Chemical Theory and Computation, 17(4), 2294-2306. American Chemical Society
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation
With the continual improvement of computing hardware and algorithms, simulations have become a powerful tool for understanding all sorts of (bio)molecular processes. To handle the large simulation data sets and to accelerate slow, activated transitio
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a161c842f66211f9ebc11248cba86d8f
https://dare.uva.nl/personal/pure/en/publications/discovering-collective-variables-of-molecular-transitions-via-genetic-algorithms-and-neural-networks(e49565c0-ac42-4b97-a91e-b86589f6921f).html
https://dare.uva.nl/personal/pure/en/publications/discovering-collective-variables-of-molecular-transitions-via-genetic-algorithms-and-neural-networks(e49565c0-ac42-4b97-a91e-b86589f6921f).html
Autor:
Laura Pedraza-González, Ana-Nicoleta Bondar, Yigal Lahav, Igor Schapiro, Cristina E. González-Espinoza, Qays NasserEddin, Jacob Kongsted, Aditya G. Rao, Alberto Pérez de Alba Ortíz, Gil S. Amoyal, Lukas Kemmler, Anna I. Krylov, Rajiv K. Kar, Isabelle Navizet, Maria Andrea Mroginski, Avishai Barnoy, Ilia A. Solov'yov, Saumik Sen, Elisa Pieri, Xuchun Yang, Francesca Fanelli, Michalis Lazaratos, Tomasz Adam Wesolowski, Veniamin Borin, Seung Soo Kim, Massimo Olivucci, Ofer Filiba, Nicolas Ferré, Christian Wiebeler, Ronald González, Luca De Vico, Young Min Rhee, Jógvan Magnus Haugaard Olsen, T. Domratcheva, Suliman Adam, Jonathan R. Church, Alexander V. Nemukhin, Niccolò Ricardi, Bernd Ensing
Publikováno v:
Mroginski, M A, Adam, S, Amoyal, G S, Barnoy, A, Bondar, A N, Borin, V A, Church, J R, Domratcheva, T, Ensing, B, Fanelli, F, Ferré, N, Filiba, O, Pedraza-González, L, González, R, González-Espinoza, C E, Kar, R K, Kemmler, L, Kim, S S, Kongsted, J, Krylov, A I, Lahav, Y, Lazaratos, M, NasserEddin, Q, Navizet, I, Nemukhin, A, Olivucci, M, Olsen, J M H, Pérez de Alba Ortíz, A, Pieri, E, Rao, A G, Rhee, Y M, Ricardi, N, Sen, S, Solov'yov, I A, De Vico, L, Wesolowski, T A, Wiebeler, C, Yang, X & Schapiro, I 2021, ' Frontiers in Multiscale Modeling of Photoreceptor Proteins ', Photochemistry and Photobiology, vol. 97, no. 2, pp. 243-269 . https://doi.org/10.1111/php.13372
Photochem Photobiol
Photochemistry and Photobiology
Photochemistry and Photobiology, Wiley, 2020, ⟨10.1111/php.13372⟩
Photochemistry and Photobiology, Vol. 97, No 2 (2021) pp. 243-269
Photochemistry and Photobiology, 2021, 97, pp.243-269. ⟨10.1111/php.13372⟩
Photochemistry and Photobiology, Wiley, 2021, 97, pp.243-269. ⟨10.1111/php.13372⟩
Photochem Photobiol
Photochemistry and Photobiology
Photochemistry and Photobiology, Wiley, 2020, ⟨10.1111/php.13372⟩
Photochemistry and Photobiology, Vol. 97, No 2 (2021) pp. 243-269
Photochemistry and Photobiology, 2021, 97, pp.243-269. ⟨10.1111/php.13372⟩
Photochemistry and Photobiology, Wiley, 2021, 97, pp.243-269. ⟨10.1111/php.13372⟩
This is the peer reviewed version of the following article: Mroginski, Adam, Amoyal, Barnoy, Bondar, ... Schapiro. (2020). Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochemistry and Photobiology, 97(2):243-269, which has been publ
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::422a02c2e99a45f84a0c0eec494e2b86
https://findresearcher.sdu.dk:8443/ws/files/180569042/php.13372.pdf
https://findresearcher.sdu.dk:8443/ws/files/180569042/php.13372.pdf
Autor:
Bernd Ensing, Dixy E. Green, Ralf P. Richter, Fouzia Bano, Alberto Pérez de Alba Ortíz, Paul L. DeAngelis, Xing Zhang, Robert J. Linhardt, Gijsje H. Koenderink, Giulia Giubertoni, Huib J. Bakker
Publikováno v:
Macromolecules
Macromolecules, 54(3)
Macromolecules, 54(3), 1137-1146. American Chemical Society
Macromolecules, 54(3)
Macromolecules, 54(3), 1137-1146. American Chemical Society
The biological functions of natural polyelectrolytes are strongly influenced by the presence of ions, which bind to the polymer chains and thereby modify their properties. Although the biological impact of such modifications is well recognized, a det
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2ad8d47d67bc85725c76c247a29dbd54
https://doi.org/10.1021/acs.macromol.0c02242
https://doi.org/10.1021/acs.macromol.0c02242
Autor:
Pérez de Alba Ortíz, A.
Advances in the atomistic understanding of biomolecular structure and function come with wide applications in medicine, pharmacology and biomaterials, as well as with fundamental answers about the nature of living things. Such insight can in principl
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=narcis______::6332124b426ea5c9194d92f81a016755
https://dare.uva.nl/personal/pure/en/publications/traversing-the-freeenergy-pathways-of-intricate-biomolecular-processes(7560b02a-7176-4fd4-b370-05f9244dc35e).html
https://dare.uva.nl/personal/pure/en/publications/traversing-the-freeenergy-pathways-of-intricate-biomolecular-processes(7560b02a-7176-4fd4-b370-05f9244dc35e).html