| Unraveling the role of protein dynamics in dihydrofolate reductase catalysis LYP Luk, J Javier Ruiz-Pernia, WM Dawson, M Roca, EJ Loveridge, ... Proceedings of the National Academy of Sciences 110 (41), 16344-16349, 2013 | 149 | 2013 |
| Unraveling the SARS-CoV-2 main protease mechanism using multiscale methods CA Ramos-Guzmán, JJ Ruiz-Pernía, I Tuñón ACS catalysis 10 (21), 12544-12554, 2020 | 122 | 2020 |
| Hybrid QM/MM potentials of mean force with interpolated corrections JJ Ruiz-Pernía, E Silla, I Tuñón, S Martí, V Moliner The Journal of Physical Chemistry B 108 (24), 8427-8433, 2004 | 122 | 2004 |
| Translocation of enzymes into a mesoporous MOF for enhanced catalytic activity under extreme conditions J Navarro-Sánchez, N Almora-Barrios, B Lerma-Berlanga, JJ Ruiz-Pernía, ... Chemical Science 10 (14), 4082-4088, 2019 | 87 | 2019 |
| Hybrid quantum mechanics/molecular mechanics simulations with two-dimensional interpolated corrections: application to enzymatic processes JJ Ruiz-Pernía, E Silla, I Tuñón, S Martí The Journal of Physical Chemistry B 110 (35), 17663-17670, 2006 | 75 | 2006 |
| Increased Dynamic Effects in a Catalytically Compromised Variant of Escherichia coli Dihydrofolate Reductase JJ Ruiz-Pernia, LYP Luk, R García-Meseguer, S Martí, EJ Loveridge, ... Journal of the American Chemical Society 135 (49), 18689-18696, 2013 | 69 | 2013 |
| Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates R García-Meseguer, S Martí, JJ Ruiz-Pernía, V Moliner, I Tuñón Nature Chemistry 5 (7), 566-571, 2013 | 67 | 2013 |
| Dynamic effects on reaction rates in a Michael addition catalyzed by chalcone isomerase. Beyond the frozen environment approach JJ Ruiz-Pernía, I Tuñón, V Moliner, JT Hynes, M Roca Journal of the American Chemical Society 130 (23), 7477-7488, 2008 | 67 | 2008 |
| Heavy enzymes—experimental and computational insights in enzyme dynamics K Świderek, JJ Ruiz-Pernía, V Moliner, I Tunon Current Opinion in Chemical Biology 21, 11-18, 2014 | 48 | 2014 |
| A microscopic description of SARS-CoV-2 main protease inhibition with Michael acceptors. Strategies for improving inhibitor design CA Ramos-Guzmán, JJ Ruiz-Pernía, I Tuñón Chemical Science 12 (10), 3489-3496, 2021 | 47 | 2021 |
| Toward an automatic determination of enzymatic reaction mechanisms and their activation free energies K Zinovjev, JJ Ruiz-Pernía, I Tunon Journal of Chemical Theory and Computation 9 (8), 3740-3749, 2013 | 44 | 2013 |
| Computational mutagenesis reveals the role of active-site tyrosine in stabilising a boat conformation for the substrate: QM/MM molecular dynamics studies of wild-type and … MES Soliman, GD Ruggiero, JJR Pernía, IR Greig, IH Williams Organic & biomolecular chemistry 7 (3), 460-468, 2009 | 44 | 2009 |
| Multiscale simulations of SARS-CoV-2 3CL protease inhibition with aldehyde derivatives. Role of protein and inhibitor conformational changes in the reaction mechanism CA Ramos-Guzmán, JJ Ruiz-Pernía, I Tuñón ACS catalysis 11 (7), 4157-4168, 2021 | 43 | 2021 |
| Chemical ligation and isotope labeling to locate dynamic effects during catalysis by dihydrofolate reductase LYP Luk, JJ Ruiz‐Pernía, AS Adesina, EJ Loveridge, I Tuñón, V Moliner, ... Angewandte Chemie 127 (31), 9144-9148, 2015 | 43 | 2015 |
| Activation free energy of catechol O-methyltransferase. Corrections to the potential of mean force M Roca, V Moliner, JJ Ruiz-Pernía, E Silla, I Tuñón The Journal of Physical Chemistry A 110 (2), 503-509, 2006 | 41 | 2006 |
| Computational simulations on the binding and reactivity of a nitrile inhibitor of the SARS-CoV-2 main protease CA Ramos-Guzmán, JJ Ruiz-Pernía, I Tuñón Chemical Communications 57 (72), 9096-9099, 2021 | 40 | 2021 |
| Protein Isotope Effects in Dihydrofolate Reductase From Geobacillus stearothermophilus Show Entropic–Enthalpic Compensatory Effects on the Rate Constant LYP Luk, JJ Ruiz-Pernía, WM Dawson, EJ Loveridge, I Tuñón, V Moliner, ... Journal of the American Chemical Society 136 (49), 17317-17323, 2014 | 39 | 2014 |
| Hydrolysis of phosphotriesters: a theoretical analysis of the enzymatic and solution mechanisms V López‐Canut, JJ Ruiz‐Pernía, R Castillo, V Moliner, I Tuñón Chemistry–A European Journal 18 (31), 9612-9621, 2012 | 35 | 2012 |
| Hybrid schemes based on quantum mechanics/molecular mechanics simulations: Goals to success, problems, and perspectives S Ferrer, J Ruiz-Pernia, S Marti, V Moliner, I Tuñón, J Bertran, J Andres Advances in protein chemistry and structural biology 85, 81-142, 2011 | 35 | 2011 |
| Mechanism of glycoside hydrolysis: A comparative QM/MM molecular dynamics analysis for wild type and Y69F mutant retaining xylanases MES Soliman, JJR Pernía, IR Greig, IH Williams Organic & Biomolecular Chemistry 7 (24), 5236-5244, 2009 | 33 | 2009 |
