Pablo D. Dans

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Modesto OrozcoProfessor of Biochemistry, Universtity of Barcelona and Group Leader IRB BarcelonaVerified email at irbbarcelona.org
Ivan Ivani, PhDIRB BarcelonaVerified email at irbbarcelona.org
Adam HOSPITALResearch Software Engineer, IRB BarcelonaVerified email at irbbarcelona.org
Federica BattistiniPost doc, IRB Barcelona ; Prof. Associat UB BarcelonaVerified email at irbbarcelona.org
Josep Ll. GelpíProfessor of Biochemistry and Molecular Biology. University of Barcelona - BSC - INB - ELIXIR-ESVerified email at ub.edu
Alberto PerezUniversity of Florida, Department of ChemistryVerified email at chem.ufl.edu
Carlos González (0000-0001-8796-1...Research Professor at CSIC.Verified email at iqfr.csic.es
Sergio PantanoInstitut Pasteur de MontevideoVerified email at pasteur.edu.uy
Richard LaveryIBCP, CNRS / University of LyonVerified email at ibcp.fr
Guillem PortellaAstraZenecaVerified email at astrazeneca.com
Matias R. MachadoInstitut Pasteur de MontevideoVerified email at pasteur.edu.uy
Agnes NoyUniversity of YorkVerified email at york.ac.uk
Pau AndrioResearch Support Engineer, Barcelona Supercomputing CenterVerified email at bsc.es
David A CaseRutgers UniversityVerified email at biomaps.rutgers.edu
Michele VendruscoloProfessor of Biophysics, University of CambridgeVerified email at cam.ac.uk
Sarah HarrisLecturer in Biological Physics, University of LeedsVerified email at leeds.ac.uk
John H. MaddocksProfessor of Mathematics, EPFLVerified email at epfl.ch
Diana BuitragoUniversidad Autónoma de ManizalesVerified email at irbbarcelona.org
Marco PasiLaboratoire de Biologie et Pharmacologie Appliquée - ENS Paris-SaclayVerified email at ens-paris-saclay.fr
Isabelle Brun HeathIRB barcelonaVerified email at irbbarcelona.org

Pablo D. Dans

Department of Biological Sciences (CENUR Litoral Norte - UdelaR) & Institut Pasteur de Montevideo

Verified email at pasteur.edu.uy - Homepage

Computational Biophysics Computational Chemistry Structural Bioinformatics Multiscale Modelling


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Parmbsc1: a refined force field for DNA simulations I Ivani, PD Dans, A Noy, A Pérez, I Faustino, J Walther, P Andrio, R Goñi, ... Nature methods 13 (1), 55, 2016	1007*	2016
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA M Pasi, JH Maddocks, D Beveridge, TC Bishop, DA Case, T Cheatham III, ... Nucleic acids research 42 (19), 12272-12283, 2014	227	2014
Direct measurement of the dielectric polarization properties of DNA A Cuervo, PD Dans, JL Carrascosa, M Orozco, G Gomila, L Fumagalli Proceedings of the National Academy of Sciences 111 (35), E3624-E3630, 2014	214	2014
Multiscale simulation of DNA PD Dans, J Walther, H Gómez, M Orozco Current opinion in structural biology 37, 29-45, 2016	181	2016
A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics PD Dans, A Zeida, MR Machado, S Pantano Journal of chemical theory and computation 6 (5), 1711-1725, 2010	169	2010
Another coarse grain model for aqueous solvation: WAT FOUR? L Darré, MR Machado, PD Dans, FE Herrera, S Pantano Journal of Chemical Theory and Computation 6 (12), 3793-3807, 2010	162	2010
The structural impact of DNA mismatches G Rossetti, PD Dans, I Gomez-Pinto, I Ivani, C Gonzalez, M Orozco Nucleic acids research 43 (8), 4309-4321, 2015	160	2015
Connecting proline and γ-aminobutyric acid in stressed plants through non-enzymatic reactions S Signorelli, PD Dans, EL Coitiño, O Borsani, J Monza PLoS One 10 (3), e0115349, 2015	155	2015
Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program M Janin, V Ortiz-Barahona, MC de Moura, A Martínez-Cardús, ... Acta Neuropathologica, 1-22, 2019	151	2019
How accurate are accurate force-fields for B-DNA? PD Dans, I Ivani, A Hospital, G Portella, C González, M Orozco Nucleic Acids Research 45 (7), 4217-4230, 2017	145*	2017
Long-timescale dynamics of the Drew–Dickerson dodecamer PD Dans, L Danilāne, I Ivani, T Dršata, F Lankaš, A Hospital, J Walther, ... Nucleic Acids Research 44 (9), 4052-4066, 2016	130*	2016
Glyceraldehyde-3-phosphate dehydrogenase is a chaperone that allocates labile heme in cells EA Sweeny, AB Singh, R Chakravarti, O Martinez-Guzman, A Saini, ... Journal of Biological Chemistry 293 (37), 14557-14568, 2018	113	2018
Impact of DNA methylation on 3D genome structure D Buitrago, M Labrador, JP Arcon, R Lema, O Flores, A Esteve-Codina, ... Nature Communication 12, 3243, 2021	102	2021
Exploring polymorphisms in B-DNA helical conformations PD Dans, A Perez, I Faustino, R Lavery, M Orozco Nucleic acids research 40 (21), 10668-10678, 2012	97	2012
Unraveling the sequence-dependent polymorphic behavior of d (CpG) steps in B-DNA PD Dans, I Faustino, F Battistini, K Zakrzewska, R Lavery, M Orozco Nucleic acids research 42 (18), 11304-11320, 2014	89	2014
Switching reversibility to irreversibility in glycogen synthase kinase 3 inhibitors: clues for specific design of new compounds DI Perez, V Palomo, C Pérez, C Gil, PD Dans, FJ Luque, S Conde, ... Journal of Medicinal Chemistry 54 (12), 4042-4056, 2011	89	2011
Saturation of recognition elements blocks evolution of new tRNA identities A Saint-Léger, C Bello, PD Dans, AG Torres, EM Novoa, N Camacho, ... Science advances 2 (4), e1501860, 2016	59	2016
A hybrid all-atom/coarse grain model for multiscale simulations of DNA MR Machado, PD Dans, S Pantano Physical Chemistry Chemical Physics 13 (40), 18134-18144, 2011	59	2011
BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data A Hospital, P Andrio, C Cugnasco, L Codo, Y Becerra, PD Dans, ... Nucleic acids research 44 (D1), D272-D278, 2016	54	2016
Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations A Zeida, MR Machado, PD Dans, S Pantano Physical Review E—Statistical, Nonlinear, and Soft Matter Physics 86 (2 …, 2012	51	2012

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