| 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 | 3462 | 2021 |
| Cholesterol biosynthesis: a mechanistic overview NM Cerqueira, EF Oliveira, DS Gesto, D Santos-Martins, C Moreira, ... Biochemistry 55 (39), 5483-5506, 2016 | 384 | 2016 |
| AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins D Santos-Martins, S Forli, MJ Ramos, AJ Olson Journal of chemical information and modeling 54 (8), 2371-2379, 2014 | 273 | 2014 |
| Accelerating AutoDock4 with GPUs and Gradient-Based Local Search D Santos-Martins, L Solis-Vasquez, AF Tillack, MF Sanner, A Koch, S Forli Journal of chemical theory and computation 17 (2), 1060-1073, 2021 | 263 | 2021 |
| Supercomputer-based ensemble docking drug discovery pipeline with application to COVID-19 A Acharya, R Agarwal, MB Baker, J Baudry, D Bhowmik, S Boehm, ... Journal of chemical information and modeling 60 (12), 5832-5852, 2020 | 178 | 2020 |
| SuFEx-enabled, agnostic discovery of covalent inhibitors of human neutrophil elastase Q Zheng, JL Woehl, S Kitamura, D Santos-Martins, CJ Smedley, G Li, ... Proceedings of the National Academy of Sciences 116 (38), 18808-18814, 2019 | 171 | 2019 |
| Receptor-based virtual screening protocol for drug discovery NM Cerqueira, D Gesto, EF Oliveira, D Santos-Martins, NF Brás, ... Archives of biochemistry and biophysics 582, 56-67, 2015 | 160 | 2015 |
| Structural basis for strand-transfer inhibitor binding to HIV intasomes DO Passos, M Li, IK Jóźwik, XZ Zhao, D Santos-Martins, R Yang, SJ Smith, ... Science 367 (6479), 810-814, 2020 | 100 | 2020 |
| Enzymatic flexibility and reaction rate: a QM/MM study of HIV-1 protease AJM Ribeiro, D Santos-Martins, N Russo, MJ Ramos, PA Fernandes Acs Catalysis 5 (9), 5617-5626, 2015 | 89 | 2015 |
| GPU-accelerated drug discovery with docking on the summit supercomputer: Porting, optimization, and application to COVID-19 research S LeGrand, A Scheinberg, AF Tillack, M Thavappiragasam, JV Vermaas, ... Proceedings of the 11th ACM international conference on bioinformatics …, 2020 | 75 | 2020 |
| 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 | 65 | 2019 |
| Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase … AL Perryman, DN Santiago, S Forli, D Santos-Martins, AJ Olson Journal of computer-aided molecular design 28, 429-441, 2014 | 58 | 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 | 54 | |
| Mechanistic pathway on human α-glucosidase maltase-glucoamylase Unveiled by QM/MM calculations NF Brás, D Santos-Martins, PA Fernandes, MJ Ramos The Journal of Physical Chemistry B 122 (14), 3889-3899, 2018 | 35 | 2018 |
| Benchmarking the performance of irregular computations in AutoDock-GPU molecular docking L Solis-Vasquez, AF Tillack, D Santos-Martins, A Koch, S LeGrand, S Forli Parallel computing 109, 102861, 2022 | 31 | 2022 |
| Discovery of potent coumarin-based kinetic stabilizers of amyloidogenic immunoglobulin light chains using structure-based design NL Yan, D Santos-Martins, R Nair, A Chu, IA Wilson, KA Johnson, S Forli, ... Journal of medicinal chemistry 64 (9), 6273-6299, 2021 | 28 | 2021 |
| A buried water molecule influences reactivity in α-amylase on a subnanosecond time scale D Santos-Martins, AR Calixto, PA Fernandes, MJ Ramos ACS Catalysis 8 (5), 4055-4063, 2018 | 26 | 2018 |
| HMG-CoA Reductase inhibitors: an updated review of patents of novel compounds and formulations (2011-2015) EF Oliveira, D Santos-Martins, AM Ribeiro, NF Brás, NS Cerqueira, ... Expert opinion on therapeutic patents 26 (11), 1257-1272, 2016 | 25 | 2016 |
| Structural basis for the stabilization of amyloidogenic immunoglobulin light chains by hydantoins NL Yan, D Santos-Martins, E Rennella, BB Sanchez, JS Chen, LE Kay, ... Bioorganic & medicinal chemistry letters 30 (16), 127356, 2020 | 21 | 2020 |
| 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 |
Stefano ForliScripps Research, Dep. Integrative Structural Computational Biology @ForliLabVerified email at scripps.edu