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Frontiers in Multiscale Modeling of Photoreceptor Proteins.
Photochem Photobiol. 2021 Mar;97(2):243-269. doi: 10.1111/php.13372. Epub 2021 Feb 13.
Photochem Photobiol. 2021.
PMID: 33369749
Free PMC article.
Review.
The Adaptive Path Collective Variable: A Versatile Biasing Approach to Compute the Average Transition Path and Free Energy of Molecular Transitions.
Pérez de Alba Ortíz A, Vreede J, Ensing B.
Pérez de Alba Ortíz A, et al.
Methods Mol Biol. 2019;2022:255-290. doi: 10.1007/978-1-4939-9608-7_11.
Methods Mol Biol. 2019.
PMID: 31396907
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Discovering Collective Variables of Molecular Transitions via Genetic Algorithms and Neural Networks.
Hooft F, Pérez de Alba Ortíz A, Ensing B.
Hooft F, et al. Among authors: perez de alba ortiz a.
J Chem Theory Comput. 2021 Apr 13;17(4):2294-2306. doi: 10.1021/acs.jctc.0c00981. Epub 2021 Mar 4.
J Chem Theory Comput. 2021.
PMID: 33662202
Free PMC article.
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Sequence dependence of transient Hoogsteen base pairing in DNA.
Pérez de Alba Ortíz A, Vreede J, Ensing B.
Pérez de Alba Ortíz A, et al.
PLoS Comput Biol. 2022 May 26;18(5):e1010113. doi: 10.1371/journal.pcbi.1010113. eCollection 2022 May.
PLoS Comput Biol. 2022.
PMID: 35617357
Free PMC article.
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Peptide Side-COOH Groups Have Two Distinct Conformations under Biorelevant Conditions.
Sofronov OO, Giubertoni G, Pérez de Alba Ortíz A, Ensing B, Bakker HJ.
Sofronov OO, et al. Among authors: perez de alba ortiz a.
J Phys Chem Lett. 2020 May 7;11(9):3466-3472. doi: 10.1021/acs.jpclett.0c00711. Epub 2020 Apr 21.
J Phys Chem Lett. 2020.
PMID: 32293901
Free PMC article.
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Advances in enhanced sampling along adaptive paths of collective variables.
Pérez de Alba Ortíz A, Tiwari A, Puthenkalathil RC, Ensing B.
Pérez de Alba Ortíz A, et al.
J Chem Phys. 2018 Aug 21;149(7):072320. doi: 10.1063/1.5027392.
J Chem Phys. 2018.
PMID: 30134692
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Strong Reduction of the Chain Rigidity of Hyaluronan by Selective Binding of Ca2+ Ions.
Giubertoni G, Pérez de Alba Ortíz A, Bano F, Zhang X, Linhardt RJ, Green DE, DeAngelis PL, Koenderink GH, Richter RP, Ensing B, Bakker HJ.
Giubertoni G, et al. Among authors: perez de alba ortiz a.
Macromolecules. 2021 Feb 9;54(3):1137-1146. doi: 10.1021/acs.macromol.0c02242. Epub 2021 Jan 19.
Macromolecules. 2021.
PMID: 33583956
Free PMC article.
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Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA.
Vreede J, Pérez de Alba Ortíz A, Bolhuis PG, Swenson DWH.
Vreede J, et al. Among authors: perez de alba ortiz a.
Nucleic Acids Res. 2019 Dec 2;47(21):11069-11076. doi: 10.1093/nar/gkz837.
Nucleic Acids Res. 2019.
PMID: 31665440
Free PMC article.
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