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: participation in the SAMPL4 protein-ligand binding challenge. - Alexander L. Perryman; Daniel N. Santiago; Stefano Forli; Diogo Santos-Martins; Arthur J. Olson (J. Comput. Aided Mol. Des., 2014)

AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins. - Diogo Santos-Martins; Stefano Forli; Maria João Ramos; Arthur J. Olson (J. Chem. Inf. Model., 2014)

Interaction with specific HSP90 residues as a scoring function: validation in the D3R Grand Challenge 2015. - Diogo Santos-Martins (J. Comput. Aided Mol. Des., 2016)

Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas. - Diogo Santos-Martins; Pedro Alexandrino Fernandes; Maria João Ramos (J. Comput. Aided Mol. Des., 2016)

Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4. - Lea El-Khoury; Diogo Santos-Martins; Sukanya Sasmal; Jérôme Eberhardt; Giulia Bianco; Francesca Alessandra Ambrosio; Leonardo Solis-Vasquez; Andreas Koch 001; Stefano Forli; David L. Mobley (J. Comput. Aided Mol. Des., 2019)

D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU. - Diogo Santos-Martins; Jérôme Eberhardt; Giulia Bianco; Leonardo Solis-Vasquez; Francesca Alessandra Ambrosio; Andreas Koch 001; Stefano Forli (J. Comput. Aided Mol. Des., 2019)

GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research. - Scott LeGrand; Aaron Scheinberg; Andreas F. Tillack; Mathialakan Thavappiragasam; Josh Vincent Vermaas; Rupesh Agarwal; Jeff Larkin; Duncan Poole; Diogo Santos-Martins; Leonardo Solis-Vasquez; Andreas Koch 001; Stefano Forli; et al. (BCB, 2020)

Evaluating the Energy Efficiency of OpenCL-accelerated AutoDock Molecular Docking. - Leonardo Solis-Vasquez; Diogo Santos-Martins; Andreas Koch 001; Stefano Forli (PDP, 2020)

Parallelizing Irregular Computations for Molecular Docking. - Leonardo Solis-Vasquez; Diogo Santos-Martins; Andreas F. Tillack; Andreas Koch 001; Jérôme Eberhardt; Stefano Forli (IA3@SC, 2020)

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. - Atanu Acharya; Rupesh Agarwal; Matthew B. Baker; Jérôme Baudry; Debsindhu Bhowmik; Swen Böhm; Kendall G. Byler; Sam Yen-Chi Chen; Leighton Coates; Connor J. Cooper; Omar Demerdash; Isabella Daidone; et al. (J. Chem. Inf. Model., 2020)

AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. - Jérôme Eberhardt; Diogo Santos-Martins; Andreas F. Tillack; Stefano Forli (J. Chem. Inf. Model., 2021)

Benchmarking the performance of irregular computations in AutoDock-GPU molecular docking. - Leonardo Solis-Vasquez; Andreas F. Tillack; Diogo Santos-Martins; Andreas Koch 001; Scott LeGrand; Stefano Forli (Parallel Comput., 2022)

Ringtail: A Python Tool for Efficient Management and Storage of Virtual Screening Results. - Althea T. Hansel-Harris; Diogo Santos-Martins; Niccolò Bruciaferri; Andreas F. Tillack; Matthew Holcomb; Stefano Forli (J. Chem. Inf. Model., 2023)

Reactive Docking: A Computational Method for High-Throughput Virtual Screenings of Reactive Species. - Giulia Bianco; Matthew Holcomb; Diogo Santos-Martins; Andreas F. Tillack; Althea T. Hansel-Harris; Stefano Forli (J. Chem. Inf. Model., 2023)

CosolvKit: a Versatile Tool for Cosolvent MD Preparation and Analysis. - Niccolò Bruciaferri; Jérôme Eberhardt; Manuel A. Llanos; Johannes R. Loeffler; Matthew Holcomb; Monica L. Fernández-Quintero; Diogo Santos-Martins; Andrew B. Ward; Stefano Forli (J. Chem. Inf. Model., 2024)