Biblio

Formation of left-handed helices by C2′-fluorinated nucleic acids under physiological salt conditions, El-Khoury, Roberto, Cabrero Cristina, Movilla Santiago, Kaur Harneesh, Friedland David, Domínguez Arnau, Thorpe James D., Roman Morgane, Orozco Modesto, González Carlos, et al. , Nucleic Acids Research, 06/2024, Volume 52, Issue 13, p.7414 - 7428, (2024)

An integrated machine-learning model to predict nucleosome architecture, Sala, Alba, Labrador Mireia, Buitrago Diana, de Jorge Pau, Battistini Federica, Heath Isabelle Brun, and Orozco Modesto , Nucleic Acids Research, 09/2024, Volume 52, Issue 17, p.10132 - 10143, (2024)

Main role of fractal-like nature of conformational space in subdiffusion in proteins, Maggi, Luca, and Orozco Modesto , Physical Review E, 03/2024, Volume 109, Issue 3, p.034402, (2024)

MD-DATA: the legacy of the ABC Consortium, Hospital, Adam, and Orozco Modesto , Biophysical Reviews, 04/2024, (2024)

Molecular stripping underpins derepression of a toxin–antitoxin system, Grabe, Grzegorz J., Giorgio Rachel T., Wieczór Miłosz, Gollan Bridget, Sargen Molly, Orozco Modesto, Hare Stephen A., and Helaine Sophie , Nat Struct Mol Biol, 2024/03/27, (2024)

A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort, Beltrán, Daniel, Hospital Adam, Gelpí Josep Lluis, and Orozco Modesto , Nucleic Acids Res, 04/2024, Volume 52, Issue D1, p.D393 - D403, (2024)

Nucleic acids in modern molecular therapies: A realm of opportunities for strategic drug design, Genna, Vito, Reyes-Fraile Laura, Iglesias-Fernández Javier, and Orozco Modesto , Current Opinion in Structural Biology, 08/2024, Volume 87, p.102838, (2024)

The Rhodium Analogue of Coenzyme B12 as an Anti-Photoregulatory Ligand Inhibiting Bacterial CarH Photoreceptors, Pérez-Castaño, Ricardo, Aranda Juan, Widner Florian J., Kieninger Christoph, Deery Evelyne, Warren Martin J., Orozco Modesto, Elías-Arnanz Montserrat, Padmanabhan S., and Kräutler Bernhard , Angewandte Chemie International Edition, 04/2024, Volume 63, Issue 18, p.e202401626, (2024)

RNA dynamics from experimental and computational approaches, Bussi, Giovanni, Bonomi Massimiliano, Gkeka Paraskevi, Sattler Michael, Al-Hashimi Hashim M., Auffinger Pascal, Duca Maria, Foricher Yann, Incarnato Danny, Jones Alisha N., et al. , Structure, 09/2024, Volume 32, Issue 9, p.1281 - 1287, (2024)

SETD8 inhibition targets cancer cells with increased rates of ribosome biogenesis, Murga, Matilde, Lopez-Pernas Gema, Soliva Robert, Fueyo-Marcos Elena, Amor Corina, Faustino Ignacio, Serna Marina, Serrano Alicia G., Díaz Lucía, Martínez Sonia, et al. , Cell Death & Disease, 09/2024, Volume 15, Issue 9, p.694, (2024)

Site-specific incorporation of a fluorescent nucleobase analog enhances i-motif stability and allows monitoring of i-motif folding inside cells, Mir, Bartomeu, Serrano-Chacón Israel, Medina Pedro, Macaluso Veronica, Terrazas Montserrat, Gandioso Albert, Garavís Miguel, Orozco Modesto, Escaja Núria, and González Carlos , Nucleic Acids Res, 04/2024, Volume 52, Issue 6, p.3375 - 3389, (2024)

Special issue: Multiscale simulations of DNA from electrons to nucleosomes, Maddocks, John H., Dans Pablo D., Cheatham Thomas H., Harris Sarah, Laughton Charles, Orozco Modesto, Pollack Lois, and Olson Wilma K. , Biophysical Reviews, 06/2024, Volume 16, Issue 3, p.259 - 262, (2024)

Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows, Bayarri, Genis, Andrio Pau, Gelpí Josep Lluis, Hospital Adam, and Orozco Modesto , PLOS Computational Biology, 06/2024, Volume 20, Issue 6, p.e1012173 , (2024)

CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers, Farré-Gil, David, Bayarri Genis, Laughton Charles A., Hospital Adam, and Orozco Modesto , Nucleic Acids Research, 05/2025, Volume 53, Issue W1, p.W151 - W157, (2025)

The conserved lysine residue in transmembrane helix 5 is pivotal for the cytoplasmic gating of the L-amino acid transporters, Fort, Joana, Nicolàs-Aragó Adrià, Maggi Luca, Martinez-Molledo Maria, Kapiki Despoina, González-Novoa Paula, Gómez-Gejo Patricia, Zijlstra Niels, Bodoy Susanna, Pardon Els, et al. , PNAS Nexus, 01/2025, Volume 4, Issue 1, p.pgae584, (2025)

Flexibility in PAM recognition expands DNA targeting in xCas9, Hossain, Kazi A., Nierzwicki Lukasz, Orozco Modesto, Czub Jacek, and Palermo Giulia , eLife, 02/2025, Volume 13, p.RP102538, (2025)

Gromologist: A GROMACS-oriented utility library for structure and topology manipulation, Wieczór, Miłosz, Czub Jacek, and Orozco Modesto , SoftwareX, 05/2025, Volume 30, p.102118, (2025)

Naphthalene diimide-naphthalimide dyads promote telomere damage by selectively targeting multimeric G-quadruplexes, Pirota, Valentina, Iachettini Sara, Platella Chiara, Zizza Pasquale, Fracchioni Giorgia, Di Vito Serena, Carachino Alice, Battistini Federica, Orozco Modesto, Freccero Mauro, et al. , Nucleic Acids Research, 04/2025, Volume 53, Issue 7, p.gkaf301, (2025)

The need to implement FAIR principles in biomolecular simulations, Amaro, Rommie E., Åqvist Johan, Bahar Ivet, Battistini Federica, Bellaiche Adam, Beltrán Daniel, Biggin Philip C., Bonomi Massimiliano, Bowman Gregory R., Bryce Richard A., et al. , Nature Methods, 04/2025, Volume 22, Issue 4, p.641 - 645, (2025)

Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism, Genna, Vito, Portella Guillem, Sala Alba, Terrazas Montserrat, Serrano-Chacón Israel, González Javier, Villegas Núria, Mateo Lidia, Castellazzi Chiara, Labrador Mireia, et al. , Nucleic Acids Research, 03/2025, Volume 53, Issue 5, p.gkaf170, (2025)