Embedded Files
LiST OF PUBLICATIONS
LiST OF PUBLICATIONS
- Olivia Love, Rodrigo Galindo-Murillo, Daniel R. Roe, Pablo D. Dans, Thomas E. Cheatham III, Christina Bergonzo. modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields. Journal of Chemical Theory and Computation. 20, 9354-9363 (2024). (IF 2023: 5.700) PDF
- Gabriela da Rosa, Leandro Grille, Pablo D. Dans. Ramachandran-like Conformational Space for DNA. Journal of Chemical Information and Modeling. 64, 8339-8348 (2024) CORRESPONDING AUTHOR. (IF 2023: 5.700) PDF
- John H Maddocks, Pablo D Dans, Thomas H Cheatham III, Sarah Harris, Charlie Laughton, Modesto Orozco, Lois Pollack, Wilma K Olson. Multiscale simulations of DNA from electrons to nucleosomes. Biophysical Reviews. https://doi.org/10.1007/s12551-024-01204-7 (2024). (IF 2021: 4.430) PDF
- Pablo D Dans. Multiscale simulations of DNA from electrons to nucleosomes: 22 years of the Ascona B-DNA Consortium. Biophysical Reviews. https://doi.org/10.1007/s12551-024-01194-6 (2024). (IF 2021: 4.430) PDF
- Wilma K Olson, John H Maddocks, Pablo D Dans, Thomas H Cheatham III, Sarah Harris, Charlie Laughton, Modesto Orozco, Lois Pollack. An open call for contributions to a special issue of Biophysical Reviews focused on multiscale simulations of DNA from electrons to nucleosomes. Biophysical Reviews. 15 (6), 1901-1902 (2023). (IF 2021: 4.430) PDF
- N. Parisis, Pablo D. Dans, M. Jbara, B. Singh, D. Schusi-Tiffoche, et al. Histone H3 serine-57 is a CHK1 substrate whose phosphorylation affects DNA repair. Nature Communications 14 (1), 5104 (2023). (IF 2022: 17.694) PDF
- Leandro Grille, Diego Gallego, Leonardo Darré, Gabriela da Rosa, Federica Battistini, Modesto Orozco, Pablo D. Dans. The Pseudo-Torsional Space of RNA. RNA Journal, 29 (12), 1896-1909 (2023) CORRESPONDING AUTHOR. (IF 2022: 5.636) PDF
- Gabriela Llauger, Roberto Melero, Demián Monti, Gabriela Sycz, Cristián Huck-Iriart, María L Cerutti, Sebastián Klinke, Evelyn Mikkelsen, Ariel Tijman, Rocío Arranz, Victoria Alfonso, Sofía M Arellano, Fernando A Goldbaum, Yann GJ Sterckx, José-María Carazo, Sergio B Kaufman, Pablo D Dans, Mariana del Vas, Lisandro H Otero. A fijivirus major viroplasm protein shows RNA-stimulated ATPase activity by adopting pentameric and hexameric assemblies of dimers. Mbio, e00023-23 (2023). (IF 2022: 7.867) PDF
- Neguembor Maria Victoria, Buitrago Diana, Lema Rafael, Arcon Juan Pablo, Walther Jürgen, Garate Ximena, Martin Laura, Romero Pablo, Gut Marta, Blanc Julie, AlHaj Abed Jumana, Lakadamyali Melike, Wu Chao-ting, Brun Heath Isabelle, Orozco Modesto, Dans Pablo D., and Cosma Maria Pia. MioS, an integrated imaging and modeling strategy to resolve gene folding at basepair resolution. Nature Structural and Molecular Biology, 29 (10), 1011-1023 (2022) CORRESPONDING AUTHOR (IF 2020: 15.369) PDF
- Martin Benjamin, Dans Pablo D., Wieczor Milosz, Villegas Nuria, Brun-Heath Isabelle, Battistini Federica, Terrazas Montserrat, and Orozco Modesto. Molecular basis of Arginine and Lysine DNA sequence-dependent thermos-stability modulation. PLOS Computational Biology. DOI: 10.1371/journal.pcbi.1009749 (2022) CORRESPONDING AUTHOR (IF 2018: 4.428) PDF
- da Rosa Gabriela, Grille Leandro, Calzada Victoria, ABC consortium and Dans Pablo D. Sequence-Dependent Structural Properties of B-DNA: What Have We Learned in 40 Years? Biophysical Reviews. DOI: 10.1007/s12551-021-00893-8 (2021) CORRESPONDING AUTHOR (IF 2021: 4.430) PDF
- Battistini Federica, Dans Pablo D., Terrazas Montserrat, Castellazzi Chiara L., Portella Guillem, Labrador Mireia, Villegas Núria, Brun-Heath Isabelle, Gómez-Pinto Irene, González Carlos and Orozco Modesto. The Impact of the Hydroxymethylcytosine Epigenetic Signature on DNA Structure and Function. PLOS Computational Biology, 17, e1009547. DOI: 10.1371/journal.pcbi.1009547 (2021) (IF 2018: 4.428) PDF
- Diana Buitrago, Mireia Labrador, Juan Pablo Arcon, Rafael Lema, Oscar Flores, Anna Esteve-Codina, Julie Blanc, Nuria Villegas, David Bellido, Marta Gut, Pablo D. Dans, Simon C. Heath, Ivo Gut, Isabelle Brun Heath, and Modesto Orozco. Impact of DNA methylation on 3D genome structure. Nature Communication, 12, 3243. DOI: 10.1038/s41467-021-23142-8en (2021) (IF 2020: 14.919) PDF
- Rodríguez-Decuadro Susana, da Rosa Gabriela, Radío Santiago, Barraco-Vega Mariana, Benko-Iseppon Ana Maria, Dans Pablo D., Smircich Pablo, and Cecchetto Gianna. Antimicrobial peptides in the seedling transcriptome of the tree legume Peltophorum dubium. Biochimie, DOI: 10.1016/j.biochi.2020.11.005 (2021) (IF 2019: 3.188) PDF
- Zheng Ruifang, da Rosa Gabriela, Dans Pablo D., and Peluffo R. Daniel. Molecular Determinants for Nitric Oxide Regulation of the Murine Cationic Amino Acid Transporter CAT-2A. Biochemistry, DOI: 10.1021/acs.biochem.0c00729 (2020) (IF 2020: 3.162) PDF
- Walther Jürgen, Dans Pablo D., Balaceanu Alexandra, Hospital Adam, Bayarri Genís, and Orozco Modesto. A Multi-Modal Coarse-Grain Model of DNA Flexibility Mappable to the Atomistic Level. Nucleic Acids Research, DOI: 10.1093/nar/gkaa015 (2020). CORRESPONDING AUTHOR (IF 2017: 11.561) PDF
- Dans Pablo D., Balaceanu Alexandra, Pasi Marco, Patelli Alessandro S. P, Petkevičiūtė Daiva, Walther Jürgen, Hospital Adam, Lavery Richard, Maddocks John, and Orozco Modesto. The Static and Dynamic Structural Heterogeneities of B-DNA: Extending Calladine-Dickerson rules. Nucleic Acids Research, DOI: 10.1093/nar/gkz905 (2019). CORRESPONDING AUTHOR (IF 2017: 11.561) PDF
- Maxime Janin, Vanessa Ortiz-Barahona, Manuel Castro de Moura, Anna Martínez-Cardús, Pere Llinàs-Arias, Marta Soler, Daphna Nachmani, Joffrey Pelletier, Ulrike Schumann, Maria Calleja-Cervantes, Sebastian Moran, Sonia Guil, Alberto Bueno-Costa, David Pinyeiro, Montserrat Perez-Salvia, Margalida Rosselló-Tortella, Laia Piqué, Joan Bech-Serra, Carolina De la Torre, August Vidal, María Martinez-Iniesta, Juan Martín-Tejera, Alberto Villanueva, Alexandra Arias, Isabel Cuartas, Ana Aransay, Andres Morales La Madrid, Angel Carcaboso, Vicente Santa-Maria, Jaume Mora, Agustín Fernandez, Mario Fraga, Iban Aldecoa, Leire Pedrosa, Francesc Graus, Noemi Vidal, Fina Martínez-Soler, Avelina Tortosa, Cristina Carrato, Carme Balañá, Matthew Boudreau, Paul Hergenrother, Peter Kötter, Karl-Dieter Entian, Jürgen Hench, Stephan Frank, Sheila Mansouri, Gelareh Zadeh, Pablo D. Dans, Modesto Orozco, George Thomas, Sandra Blanco, Joan Seoane, Thomas Preiss, Pier Paolo Pandolfi, Manel Esteller. Epigenetic Loss of RNA Methyltransferase NSUN5 in Glioma Targets Ribosomes to Drive a Stress Adaptive Translational Program Associated with Long-Term Survival. Acta Neuropathologica, DOI: 10.1007/s00401-019-02062-4 (2019). (IF 2017: 18.185) PDF
- Rodriguez Susana, Dans Pablo D., Borba María Alejandra, Benko-Iseppon Ana María, and Cecchetto Gianna. Gene Isolation of a New Legume Defensin with a Broad Spectrum of Antimicrobial Activity. Planta Journal, DOI: 10.1007/s00425-019-03260-w (2019). (IF 2017: 3.249) PDF
- Battistini Federica, Hospital Adam, Buitrago Diana, Dans Pablo D. Gelpi Josep Lluis, and Orozco Modesto. How B-DNA Dynamics Decipher Sequence-selective Protein Recognition. Journal of Molecular Biology, DOI: 10.1016/j.jmb.2019.07.021 (2019). (IF 2017: 5.067) PDF
- Gallego Diego, Darré Leonardo, Dans Pablo D., and Orozco Modesto. VeriNA3d: An R Package fo the Data Mining of Nucleic Acids. Bioinformatics – Application Notes, DOI: 10.1093/bioinformatics/btz553 (2019). CORRESPONDING AUTHOR (IF 2017: 4.531) PDF
- Balaceanu Alexandra, Biutrago Diana, Walther Jurgen, Dans Pablo D., Orozco Modesto. Modulation of the Helical Properties of DNA: Next-To-Nearest Neighbour Effects and Beyond. Nucleic Acids Research, DOI: 10.1093/nar/gkz255, (2019). (IF 2017: 11.561) PDF
- Kuzmanic Antonia, Dans Pablo D., Orozco Modesto. An in-depth look at DNA crystals through the prism of molecular dynamics simulations. CHEM, Cell press, DOI: 10.1016/j.chempr.2018.12.007, (2019). (IF 2017: 14.104) PDF
- Dans Pablo D., Gallego Diego, Balaceanu Alexandra, Darré Leonardo, Gómez Hansel, and Orozco Modesto. Modeling, Simulations, and Bioinformatics at the Service of RNA Structure. CHEM, Cell press, DOI: 10.1016/j.chempr.2018.09.015, (2018). (IF 2017: 14.104) PDF
- Elizabeth Sweeny, Anuradha Singh, Ritu Chakravarti, Osiris Martinez-Guzman, Arushi Saini, Mohammad Haque, Greer Garee, Dans Pablo D., Luciana Hannibal, Amit Reddi, and Dennis Stuehr. Glyceraldehyde 3-phosphate dehydrogenase is a chaperone that allocates labile heme in cells. Journal of Biological Chemistry. DOI: 10.1074/jbc.RA118.004169, (2018). (IF 2017: 4.010) PDF
- Balaceanu Alexandra, Pérez Alberto, Dans Pablo D., and Orozco Modesto. Allosterism and Signal Transfer in DNA. Nucleic Acids Research, DOI: 10.1093/nar/gky549, (2018). (IF 2017: 11.561) PDF
- Rodríguez-Decuadro Susana, Barraco-Vega Mariana, Dans Pablo D., Pandolfi Valesca, Benko-Iseppon Ana Maria, Cecchetto Gianna., Antimicrobial and structural insights of a new snakin-like peptide isolated from Peltophorum dubium (Fabaceae). Amino Acids, DOI: 10.1007/s00726-018-2598-3, (2018). (IF 2017: 2.906) PDF
- Dans, Pablo D., Ivani Ivan, Hospital Adam, Portella Guillem, González Carlos, Orozco Modesto. How accurate are accurate force-fields for B-DNA? Nucleic Acids Research, Volume 45, Issue 7, 4217-4230, (2017). (IF 2017: 11.561) PDF
- Gómez Hansel, Walther Jürgen, Darré Leonardo, Ivani Ivan, Dans Pablo D. and Orozco Modesto. Molecular Modeling of Nucleic Acids in Computational Tools for Chemical Biology. Martín-Santamaría Sonsoles (Ed.). Royal Society of Chemistry (2017). ISBN-10: 1782627006. PDF
- Balaceanu Alexandra, Pasi Marco, Dans Pablo D., Hospital Adam, Lavery Richard, Orozco Modesto. The role of unconventional hydrogen bonds in determining BII propensities in B-DNA. Journal of Physical Chemistry Letters, Volume 8, Issue 1, 21-28, (2016). First co-author. (IF 2017: 8.709) PDF
- Darre Leonardo, Ivani Ivan, Dans Pablo D., Gómez Hansel, Hospital Adam, Orozco Modesto. Small Details Matter: the Importance of the 2’Hydroxyl in RNA. Journal of American Chemical Society, Volume 138, Issue 50, 4217-4230 (2016). (IF 2017: 14.357) PDF
- Dans Pablo D., Danilāne L., Ivani Ivan, Dršata Tomáš, Lankaš Filip, Hospital Adam, Walther Jürgen, Illa Pujagut Ricard, Battistini Federica, Gelpí Josep Lluis, Lavery Ricard and Orozco Modesto. Long-timescale dynamics of the Drew-Dickerson dodecamer. Nucleic Acids Research, Volume 44, Issue 9, 4052-4066, (2016). (IF 2017: 11.561) PDF
- Saint-Léger A., Bello-Cabrera C., Dans P.D., Torres A.G., Novoa E.M., Camacho N., Orozco M., Kondrashov, F.A. and Ribas de Pouplana L. Saturation of recognition elements blocks evolution of new tRNA identities. Science advances, Volume 2, Issue 4, e1501860, (2016). (IF 2017: 11.510) PDF
- Hospital, Adam, Andrio Pau, Cugnasco Cesare, Codó Laia, Becerra Yolanda, Dans Pablo D., Battistini Federica, Torres Jordi, Goni Ramon, Orozco Modesto, et al. BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data. Nucleic Acid Research, Volume 44, Issue D1, D272-8, (2016). (IF 2017: 11.561) PDF
- Dans, Pablo D., Walther Jurgen, Gómez Hansel, and Orozco Modesto. Multiscale simulation of DNA. Current Opinion in Structural Biology – Theory and simulation – Macromolecular machines, Volume 37, 29 – 45, (2016). (IF 2017: 7.179) PDF
- Ivani, Ivan, Dans Pablo D., Noy Agnes, Pérez Alberto, Faustino Ignacio, Hospital Adam, Walther Jurgen, Andrio Pau, Goni Ramon, Balaceanu Alexandra, et al. Parmbsc1: a refined force field for DNA simulations. Nature Methods, Volume 13, Issue 1, 55-8, (2016). First co-author. (IF 2017: 26.919) PDF
- Signorelli Santiago, Dans Pablo D., E Coitiño Laura, Borsani Omar, and Monza Jorge. Connecting proline and γ-aminobutyric acid in stressed plants through non-enzymatic reactions. PloS One, Volume 10, Issue 3, e0115349, (2015). (IF 2017: 2.766) PDF
- Rossetti Giulia, Dans Pablo D., Gómez-Pinto Irene, Ivani Ivan, González Carlos, and Orozco Modesto. The structural impact of DNA mismatches. Nucleic Acid Research, Volume 43, Issue 8, 4309-21, (2015). First co-author. (IF 2017: 11.561) PDF
- Cuervo Ana, Dans Pablo D., Carrascosa José L., Orozco Modesto, Gomila Gabriel, and Fumagalli Laura. Direct measurement of the dielectric polarization properties of DNA. Proc Natl Acad Sci U S A, Volume 111, Issue 35, E3624-30, (2014). First co-author. (IF 2017: 9.504) PDF
- Dans, Pablo D., Faustino Ignacio, Battistini Federica, Zakrzewska Krystyna, Lavery Richard, and Orozco Modesto. Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA. Nucleic Acid Research, Volume 42, Issue 19, 11304-20, (2014). (IF 2017: 11.561) PDF
- Pasi, Marco, Maddocks John H., Beveridge David, Bishop Thomas C., Case David A., Cheatham Thomas, Dans Pablo D., Jayaram B, Lankaš Filip, Laughton Charles, et al. μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acid Research, Volume 42, Issue 19, 12272-83, (2014). (IF 2017: 11.561) PDF
- Dans, Pablo D., Darré Leonardo, Machado Matias R., Zeida Ari, Brandner Astrid F., and Pantano Sergio. Assessing the Accuracy of the SIRAH Force Field to Model DNA at Coarse Grain Level. Advances in Bioinformatics and Computational Biology, 71–81, (2013). ISBN: 978-3-319-02623-7. PDF
- Zeida, Ari, Machado Matías Rodrigo, Dans Pablo D., and Pantano Sergio. Breathing, bubbling, and bending: DNA flexibility from multi microsecond simulations. Physical Review E, Volume 86, Number 2, 021903, (2012). (IF 2017: 2.284) PDF
- Dans, Pablo D., Pérez Alberto, Faustino Ignacio, Lavery Richard, and Orozco Modesto. Exploring polymorphisms in B-DNA helical conformations. Nucleic Acid Research, Volume 40, Issue 21, 10668-78, (2012). (IF 2017: 11.561) PDF
- Machado, Matías Rodrigo, Dans Pablo D., and Pantano Sergio. A hybrid all-atom/coarse grain model for multiscale simulations of DNA. Physical Chemistry Chemical Physics, Volume 13, Number 40, 18134–18144, (2011). (IF 2017: 3.906) PDF
- Perez, Daniel I., Palomo Valle, Pérez Concepción, Gil Carmen, Dans Pablo D., F Luque Javier, Conde Santiago, and Martínez Ana. Switching reversibility to irreversibility in glycogen synthase kinase 3 inhibitors: clues for specific design of new compounds. Journal of medicinal chemistry, Volume 54, Number 12, 4042–4056, (2011). (IF 2017: 6.253) PDF
- Darré, Leonardo, Machado Matias R., Dans Pablo D., Herrera Fernando E., and Pantano Sergio. Another Coarse Grain Model for Aqueous Solvation: WAT FOUR? Journal of Chemical Theory and Computation, Volume 6, Number 12, 3793–3807, (2010). (IF 2017: 5.399) PDF
- Dans, Pablo D., Zeida Ari, Machado Matías R., and Pantano Sergio. A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics. Journal of Chemical Theory and Computation, Volume 6, Number 5, 1711–1725, (2010). (IF 2017: 5.399) PDF
- Machado, Matias R., Dans Pablo D., and Pantano Sergio. Isoform-specific determinants in the HP1 binding to histone 3: insights from molecular simulations. Amino acids, Volume 38, Number 5, 1571–1581, (2010). (IF 2017: 2.906) PDF
- De Marco, Alex, Dans Pablo D., Knezevich Anna, Maiuri Paolo, Pantano Sergio, and Marcello Alessandro. Subcellular localization of the interaction between the human immunodeficiency virus transactivator Tat and the nucleosome assembly protein 1. Amino acids, Volume 38, Number 5, 1583–1593, (2010). (IF 2017: 2.906) PDF
- Dans, Pablo D., and E Coitiño Laura. Density functional theory characterization and descriptive analysis of cisplatin and related compounds. Journal of chemical information and modeling, Volume 49, Number 6, 1407–1419, (2009). (IF 2017: 3.804) PDF
- Dans Pablo D., Crespo Alejandro, Estrin Darío A., and E Coitiño Laura. Structural and Energetic Study of Cisplatin and Derivatives: Comparison of the Performance of Density Funtional Theory Implementations. Journal of Chemical Theory and Computation, Volume 4, Number 5, 740–750, (2008). (IF 2017: 5.399) PDF
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