| AutoDock Vina 1.2. 0: New docking methods, expanded force field, and python bindings J Eberhardt, D Santos-Martins, AF Tillack, S Forli Journal of chemical information and modeling 61 (8), 3891-3898, 2021 | 1930 | 2021 |
| Allostery in its many disguises: from theory to applications SJ Wodak, E Paci, NV Dokholyan, IN Berezovsky, A Horovitz, J Li, ... Structure 27 (4), 566-578, 2019 | 300 | 2019 |
| Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4 L El Khoury, D Santos-Martins, S Sasmal, J Eberhardt, G Bianco, ... Journal of computer-aided molecular design 33 (12), 1011-1020, 2019 | 57 | 2019 |
| Structural insights into the molecular mechanism of vitamin D receptor activation by lithocholic acid involving a new mode of ligand recognition AY Belorusova, J Eberhardt, N Potier, RH Stote, A Dejaegere, N Rochel Journal of Medicinal Chemistry 57 (11), 4710-4719, 2014 | 51 | 2014 |
| 1.2. 0: New docking methods, expanded force field, and python bindings., 2021, 61 J Eberhardt, D Santos-Martins, AF Tillack, SFAD Vina DOI: https://doi. org/10.1021/acs. jcim. 1c00203, 3891-3898, 0 | 35 | |
| Discovery of small-molecule enzyme activators by activity-based protein profiling BP Kok, S Ghimire, W Kim, S Chatterjee, T Johns, S Kitamura, J Eberhardt, ... Nature chemical biology 16 (9), 997-1005, 2020 | 34 | 2020 |
| Structural basis of altered potency and efficacy displayed by a major in vivo metabolite of the antidiabetic PPARγ drug pioglitazone SA Mosure, J Shang, J Eberhardt, R Brust, J Zheng, PR Griffin, S Forli, ... Journal of medicinal chemistry 62 (4), 2008-2023, 2019 | 31 | 2019 |
| New prediction categories in CASP15 A Kryshtafovych, M Antczak, M Szachniuk, T Zok, RC Kretsch, R Rangan, ... Proteins: Structure, Function, and Bioinformatics 91 (12), 1550-1557, 2023 | 22 | 2023 |
| D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU D Santos-Martins, J Eberhardt, G Bianco, L Solis-Vasquez, FA Ambrosio, ... Journal of computer-aided molecular design 33, 1071-1081, 2019 | 21 | 2019 |
| A revisited version of the apo structure of the ligand-binding domain of the human nuclear receptor retinoic X receptor α J Eberhardt, AG McEwen, W Bourguet, D Moras, A Dejaegere Acta Crystallographica Section F: Structural Biology Communications 75 (2 …, 2019 | 17 | 2019 |
| Humanized GPIbα–von Willebrand factor interaction in the mouse S Kanaji, JN Orje, T Kanaji, Y Kamikubo, Y Morodomi, Y Chen, ... Blood advances 2 (19), 2522-2532, 2018 | 14 | 2018 |
| AutoDock Vina 1.2. 0: new docking methods, expanded force field, and python bindings. 2021 J Eberhardt, D Santos-Martins, A Tillack, S Forli Publisher Full Text, 0 | 11 | |
| Assessment of protein–ligand complexes in CASP15 X Robin, G Studer, J Durairaj, J Eberhardt, T Schwede, WP Walters Proteins: Structure, Function, and Bioinformatics 91 (12), 1811-1821, 2023 | 8 | 2023 |
| Parallelizing irregular computations for molecular docking L Solis-Vasquez, D Santos-Martins, AF Tillack, A Koch, J Eberhardt, ... 2020 IEEE/ACM 10th Workshop on Irregular Applications: Architectures and …, 2020 | 6 | 2020 |
| Integrative x-ray structure and molecular modeling for the rationalization of procaspase-8 inhibitor potency and selectivity JH Xu, J Eberhardt, B Hill-Payne, GE González-Páez, JO Castellón, ... ACS chemical biology 15 (2), 575-586, 2020 | 6 | 2020 |
| Unrolr: Structural analysis of protein conformations using stochastic proximity embedding J Eberhardt, RH Stote, A Dejaegere Journal of Computational Chemistry 39 (30), 2551-2557, 2018 | 2 | 2018 |
| Automated benchmarking of combined protein structure and ligand conformation prediction M Leemann, A Sagasta, J Eberhardt, T Schwede, X Robin, J Durairaj Proteins: Structure, Function, and Bioinformatics 91 (12), 1912-1924, 2023 | 1 | 2023 |
| Automated benchmarking of combined protein structure and ligand conformation prediction X Robin, M Leemann, A Sagasta, J Eberhardt, T Schwede, J Durairaj Authorea Preprints, 2023 | 1 | 2023 |
| Comparison of ligand affinity ranking using AutoDock-GPU and MM-GBSA scores in the D3R Grand Challenge 4 L El Khoury, D Santos-Martins, S Sasmal, J Eberhardt, G Bianco, ... | 1 | 2019 |
| Combining Bayesian optimization with sequence-or structure-based strategies for optimization of protein-peptide binding J Eberhardt, A Lees, M Lill, T Schwede | | 2024 |
