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Diogo Santos-Martins
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Year
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
19092021
Cholesterol biosynthesis: a mechanistic overview
NM Cerqueira, EF Oliveira, DS Gesto, D Santos-Martins, C Moreira, ...
Biochemistry 55 (39), 5483-5506, 2016
3292016
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
2412014
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
1862021
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
1562020
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
1442019
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
1442015
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
832020
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
802015
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
722020
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
582019
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
552014
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
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
302018
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
252016
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
242018
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
232022
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
212019
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
202021
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
182020
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