| Enabling structure-based drug discovery utilizing predicted models EB Miller, H Hwang, M Shelley, A Placzek, JP Rodrigues, RK Suto, ... Cell 187 (3), 521-525, 2024 | | 2024 |
| Openmm 8: Molecular dynamics simulation with machine learning potentials P Eastman, R Galvelis, RP Peláez, CRA Abreu, SE Farr, E Gallicchio, ... The Journal of Physical Chemistry B 128 (1), 109-116, 2023 | 13 | 2023 |
| Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes via Induced Fit Docking and Free Energy Perturbation D Coskun, M Lihan, JP Rodrigues, M Vass, D Robinson, RA Friesner, ... Journal of Chemical Theory and Computation 20 (1), 477-489, 2023 | 5 | 2023 |
| An Electrostatically-steered Conformational Selection Mechanism Promotes SARS-CoV-2 Spike Protein Variation M Sorokina, J Belapure, C Tüting, R Paschke, I Papasotiriou, ... Journal of Molecular Biology 434 (13), 167637, 2022 | 2 | 2022 |
| Predicting the zoonotic capacity of mammals to transmit SARS-CoV-2 IR Fischhoff, AA Castellanos, JP Rodrigues, A Varsani, BA Han Proceedings of the Royal Society B 288 (1963), 20211651, 2021 | 83 | 2021 |
| Predicting the specificity-determining positions of receptor tyrosine kinase Axl T Karakulak, AS Rifaioglu, JP Rodrigues, E Karaca Frontiers in Molecular Biosciences 8, 658906, 2021 | 4 | 2021 |
| PDB‐tools Web: A User‐friendly Interface for the Manipulation of PDB Files B Jiménez‐García, JMC Teixeira, M Trellet, JP Rodrigues, AMJJ Bonvin Proteins: Structure, Function, and Bioinformatics 89 (3), 330-335, 2021 | 18 | 2021 |
| Predicting the Specificity-Determining Positions of Paralogous Complexes T Karakulak, AS Rifaioglu, JP Rodrigues, E Karaca bioRxiv, 2021.01. 26.428202, 2021 | 1 | 2021 |
| Insights on cross-species transmission of SARS-CoV-2 from structural modeling JP Rodrigues, S Barrera-Vilarmau, J Mc Teixeira, M Sorokina, E Seckel, ... PLoS computational biology 16 (12), e1008449, 2020 | 64 | 2020 |
| Structural models of human ACE2 variants with SARS-CoV-2 Spike protein for structure-based drug design M Sorokina, J MC Teixeira, S Barrera-Vilarmau, R Paschke, I Papasotiriou, ... Scientific data 7 (1), 309, 2020 | 25 | 2020 |
| Bacterial flagellar motor PL-ring disassembly subcomplexes are widespread and ancient M Kaplan, MJ Sweredoski, JP Rodrigues, EI Tocheva, YW Chang, ... Proceedings of the National Academy of Sciences 117 (16), 8941-8947, 2020 | 29 | 2020 |
| Interfacea: Open-Source Library for Protein Interface Analysis JPGLM Rodrigues, M Levitt Biophysical Journal 118 (3), 516a, 2020 | | 2020 |
| Less is more: coarse-grained integrative modeling of large biomolecular assemblies with HADDOCK J Roel-Touris, CG Don, R V. Honorato, JP Rodrigues, AMJJ Bonvin Journal of chemical theory and computation 15 (11), 6358-6367, 2019 | 49 | 2019 |
| Structural insights into binding specificity, efficacy and bias of a β2AR partial agonist M Masureel, Y Zou, LP Picard, E van der Westhuizen, JP Mahoney, ... Nature chemical biology 14 (11), 1059-1066, 2018 | 167 | 2018 |
| Proteomic analysis of monolayer-integrated proteins on lipid droplets identifies amphipathic interfacial α-helical membrane anchors CI Pataki, J Rodrigues, L Zhang, J Qian, B Efron, T Hastie, JE Elias, ... Proceedings of the National Academy of Sciences 115 (35), E8172-E8180, 2018 | 40 | 2018 |
| Defining distance restraints in HADDOCK AMJJ Bonvin, E Karaca, PL Kastritis, JP Rodrigues Nature protocols 13 (7), 1503-1503, 2018 | 20 | 2018 |
| Reply to ‘Defining distance restraints in HADDOCK’ Z Orban-Nemeth, R Beveridge, DM Hollenstein, E Rampler, T Stranzl, ... Nature Protocols 13 (7), 1503-1505, 2018 | 1 | 2018 |
| The solution structure of monomeric CCL 5 in complex with a doubly sulfated N‐terminal segment of CCR 5 M Abayev, JP Rodrigues, G Srivastava, B Arshava, Ł Jaremko, M Jaremko, ... The FEBS journal 285 (11), 1988-2003, 2018 | 42 | 2018 |
| SILAC-based phosphoproteomics reveals new PP2A-Cdc55-regulated processes in budding yeast B Baro, S Jativa, I Calabria, J Vinaixa, JJ Bech-Serra, C de LaTorre, ... Gigascience 7 (5), giy047, 2018 | 26 | 2018 |
| Augmenting research, education, and outreach with client-side web programming LA Abriata, JP Rodrigues, M Salathé, L Patiny Trends in biotechnology 36 (5), 473-476, 2018 | 21 | 2018 |
Alexandre M.J.J. BonvinUtrecht universityVerified email at uu.nl
