| The role of nonbonded interactions in the conformational dynamics of organophosphorous hydrolase adsorbed onto functionalized mesoporous silica surfaces DEB Gomes, RD Lins, PG Pascutti, C Lei, TA Soares The Journal of Physical Chemistry B 114 (1), 531-540, 2010 | 44 | 2010 |
| Molecular dynamics study of biomembrane/local anesthetics interactions RC Bernardi, DEB Gomes, R Gobato, CA Taft, AT Ota, PG Pascutti Molecular Physics 107 (14), 1437-1443, 2009 | 30 | 2009 |
| Dissecting a novel allosteric mechanism of cruzain: A computer-aided approach L Hernández Alvarez, DE Barreto Gomes, JE Hernandez Gonzalez, ... PLoS One 14 (1), e0211227, 2019 | 22 | 2019 |
| Protein structure prediction in the era of AI: Challenges and limitations when applying to in silico force spectroscopy PSFC Gomes, DEB Gomes, RC Bernardi Frontiers in Bioinformatics 2, 983306, 2022 | 21 | 2022 |
| Insights into the Interactions of Fasciola hepatica Cathepsin L3 with a Substrate and Potential Novel Inhibitors through In Silico Approaches L Hernandez Alvarez, D Naranjo Feliciano, JE Hernandez Gonzalez, ... PLoS neglected tropical diseases 9 (5), e0003759, 2015 | 21 | 2015 |
| The glycine receptor allosteric ligands library (GRALL) AH Cerdan, M Sisquellas, G Pereira, DE Barreto Gomes, JP Changeux, ... Bioinformatics 36 (11), 3379-3384, 2020 | 19 | 2020 |
| Molecular origins of force-dependent protein complex stabilization during bacterial infections MCR Melo, DEB Gomes, RC Bernardi Journal of the American Chemical Society 145 (1), 70-77, 2022 | 13 | 2022 |
| Theoretical studies on water–tetracaine interaction RC Bernardi, DEB Gomes, PG Pascutti, AS Ito, AT Ota International journal of quantum chemistry 106 (5), 1277-1282, 2006 | 13 | 2006 |
| Water solvent and local anesthetics: A computational study RC Bernardi, DEB Gomes, PG Pascutti, AS Ito, CA Taft, AT Ota International Journal of Quantum Chemistry 107 (7), 1642-1649, 2007 | 12 | 2007 |
| The biopaua project: A portal for molecular dynamics using grid environment A Wilter, C Osthoff, C Oliveira, DEB Gomes, E Hill, LE Dardenne, ... Advances in Bioinformatics and Computational Biology: Brazilian Symposium on …, 2005 | 10 | 2005 |
| May the force be with you: The role of hyper-mechanostability of the bone sialoprotein binding protein during early stages of Staphylococci infections PSFC Gomes, M Forrester, M Pace, DEB Gomes, RC Bernardi Frontiers in Chemistry 11, 1107427, 2023 | 9 | 2023 |
| ChemFlow─ From 2D Chemical Libraries to Protein–Ligand Binding Free Energies DE Barreto Gomes, K Galentino, M Sisquellas, L Monari, C Bouysset, ... Journal of Chemical Information and Modeling 63 (2), 407-411, 2023 | 9 | 2023 |
| Conformational variability of organophosphorus hydrolase upon soman and paraoxon binding DEB Gomes, RD Lins, PG Pascutti, C Lei, TA Soares The Journal of Physical Chemistry B 115 (51), 15389-15398, 2011 | 9 | 2011 |
| Gaussian processes regression for cyclodextrin host-guest binding prediction RM Carvalho, IGL Rosa, DEB Gomes, PVZC Goliatt, L Goliatt Journal of Inclusion Phenomena and Macrocyclic Chemistry 101, 149-159, 2021 | 8 | 2021 |
| A linear interaction energy model for cavitand host–guest binding affinities JJ Montalvo-Acosta, P Pacak, DEB Gomes, M Cecchini The Journal of Physical Chemistry B 122 (26), 6810-6814, 2018 | 8 | 2018 |
| HbMap2Grace DEB Gomes, AW Silva, RD Lins, PG Pascutti, TA Soares Software for mapping the hydrogen bond frequency, 2009 | 8 | 2009 |
| In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2 JE Hernández González, E Salas-Sarduy, L Hernández Alvarez, ... Journal of Computer-Aided Molecular Design 35, 1067-1079, 2021 | 7 | 2021 |
| Cybershuttle: An end-to-end cyberinfrastructure continuum to accelerate discovery in science and engineering S Marru, M Pierce, B Plale, S Pamidighantam, D Wannipurage, M Christie, ... Practice and Experience in Advanced Research Computing, 26-34, 2023 | 6 | 2023 |
| Deciphering molecular mechanisms stabilizing the reovirus-binding complex R dos Santos Natividade, M Koehler, PSFC Gomes, JD Simpson, ... Proceedings of the National Academy of Sciences 120 (21), e2220741120, 2023 | 6 | 2023 |
| Integrating dynamic network analysis with AI for enhanced epitope prediction in PD-L1: affibody interactions DEB Gomes, B Yang, R Vanella, MA Nash, RC Bernardi Journal of the American Chemical Society 146 (34), 23842-23853, 2024 | 5 | 2024 |
