Exploring the free energy landscape: from dynamics to networks and back D Prada-Gracia, J Gómez-Gardeñes, P Echenique, F Falo PLoS computational biology 5 (6), e1000415, 2009 | 140* | 2009 |
Efficient formalism for large scale ab initio molecular dynamics based on time-dependent density functional theory JL Alonso, X Andrade, P Echenique, F Falceto, D Prada-Gracia, A Rubio arXiv preprint arXiv:0710.3321, 2007 | 130 | 2007 |
Application of computational methods for anticancer drug discovery, design, and optimization D Prada-Gracia, S Huerta-Yépez, LM Moreno-Vargas Boletín Médico Del Hospital Infantil de México (English Edition) 73 (6), 411-423, 2016 | 114 | 2016 |
The quest for self-consistency in hydrogen bond definitions D Prada-Gracia, R Shevchuk, F Rao The Journal of chemical physics 139 (8), 2013 | 82 | 2013 |
Impact of lipid composition and receptor conformation on the spatio-temporal organization of μ-opioid receptors in a multi-component plasma membrane model KA Marino, D Prada-Gracia, D Provasi, M Filizola PLoS computational biology 12 (12), e1005240, 2016 | 52 | 2016 |
Molecular details of dimerization kinetics reveal negligible populations of transient µ-opioid receptor homodimers at physiological concentrations D Meral, D Provasi, D Prada-Gracia, J Möller, K Marino, MJ Lohse, ... Scientific reports 8 (1), 7705, 2018 | 45 | 2018 |
Structure–dynamics relationship in coherent transport through disordered systems S Mostarda, F Levi, D Prada-Gracia, F Mintert, F Rao Nature communications 4 (1), 2296, 2013 | 31 | 2013 |
Common conformational changes in flavodoxins induced by FMN and anion binding: The structure of Helicobacter pylori apoflavodoxin M Martínez‐Júlvez, N Cremades, M Bueno, I Pérez‐Dorado, C Maya, ... Proteins: Structure, function, and bioinformatics 69 (3), 581-594, 2007 | 29 | 2007 |
Mesoscopic model for free-energy-landscape analysis of DNA sequences R Tapia-Rojo, D Prada-Gracia, JJ Mazo, F Falo Physical Review E 86 (2), 021908, 2012 | 24 | 2012 |
Cloning and biochemical characterization of three glucose‑6‑phosphate dehydrogenase mutants presents in the Mexican population YY Cortés-Morales, A Vanoye-Carlo, RA Castillo-Rodríguez, ... International journal of biological macromolecules 119, 926-936, 2018 | 21 | 2018 |
Accounting for the kinetics in order parameter analysis: Lessons from theoretical models and a disordered peptide G Berezovska, D Prada-Gracia, S Mostarda, F Rao The Journal of Chemical Physics 137 (19), 2012 | 21 | 2012 |
Towards a microscopic description of the free-energy landscape of water D Prada-Gracia, R Shevchuk, P Hamm, F Rao The Journal of Chemical Physics 137 (14), 2012 | 21 | 2012 |
Consensus for the Fip35 folding mechanism? G Berezovska, D Prada-Gracia, F Rao The Journal of chemical physics 139 (3), 2013 | 20 | 2013 |
Expanding the structural diversity of DNA methyltransferase inhibitors KE Juárez-Mercado, FD Prieto-Martínez, N Sánchez-Cruz, ... Pharmaceuticals 14 (1), 17, 2020 | 18 | 2020 |
Live attenuated Salmonella enterica expressing and releasing cell-permeable Bax BH3 peptide through the MisL autotransporter system elicits antitumor activity in a murine … AA Mateos-Chávez, P Muñoz-López, EI Becerra-Báez, LF Flores-Martínez, ... Frontiers in immunology 10, 473026, 2019 | 16 | 2019 |
Biochemical Characterization and Structural Modeling of Fused Glucose-6-Phosphate Dehydrogenase-Phosphogluconolactonase from Giardia lamblia L Morales-Luna, H Serrano-Posada, A González-Valdez, ... International Journal of Molecular Sciences 19 (9), 2518, 2018 | 15 | 2018 |
Structure and dynamics of water in crowded environments slows down peptide conformational changes C Lu, D Prada-Gracia, F Rao The Journal of Chemical Physics 141 (4), 2014 | 15 | 2014 |
Water structure-forming capabilities are temperature shifted for different models R Shevchuk, D Prada-Gracia, F Rao The Journal of Physical Chemistry B 116 (25), 7538-7543, 2012 | 15 | 2012 |
A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin I from transition networks PA Cazade, W Zheng, D Prada-Gracia, G Berezovska, F Rao, C Clementi, ... The Journal of chemical physics 142 (2), 2015 | 14 | 2015 |
Macro and nano scale modelling of water–water interactions at ambient and low temperature: relaxation and residence times MC Morón, D Prada-Gracia, F Falo Physical Chemistry Chemical Physics 18 (14), 9377-9387, 2016 | 7 | 2016 |