Diogo Santos-Martins

According to our database, Diogo Santos-Martins authored at least 14 papers between 2014 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

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., September, 2023

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., April, 2023

2022

Benchmarking the performance of irregular computations in AutoDock-GPU molecular docking.

Leonardo Solis-Vasquez, Andreas F. Tillack, Diogo Santos-Martins, Andreas Koch, Scott LeGrand, Stefano Forli

Parallel Comput., 2022

2021

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

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, John D. Eblen, Sally R. Ellingson, Stefano Forli, Jens Glaser, James C. Gumbart, John Gunnels, Oscar R. Hernandez, Stephan Irle, Daniel W. Kneller, Andrey Kovalevsky, Jeffrey M. Larkin, Travis J. Lawrence, Scott LeGrand, Shih-Hsien Liu, Julie C. Mitchell, Gilchan Park, Jerry M. Parks, Anna Pavlova, Loukas Petridis, Duncan Poole, Line Pouchard, Arvind Ramanathan, David M. Rogers, Diogo Santos-Martins, Aaron Scheinberg, Ada Sedova, Yue Shen, Jeremy C. Smith, Micholas Dean Smith, Carlos Soto, Aristides Tsaris, Mathialakan Thavappiragasam, Andreas F. Tillack, Josh Vincent Vermaas, Van Quan Vuong, Junqi Yin, Shinjae Yoo, Mai Zahran, Laura Zanetti Polzi

J. Chem. Inf. Model., 2020

Parallelizing Irregular Computations for Molecular Docking.

Leonardo Solis-Vasquez, Diogo Santos-Martins, Andreas F. Tillack, Andreas Koch, Jérôme Eberhardt, Stefano Forli

Proceedings of the 10th IEEE/ACM Workshop on Irregular Applications: Architectures and Algorithms, 2020

Evaluating the Energy Efficiency of OpenCL-accelerated AutoDock Molecular Docking.

Leonardo Solis-Vasquez, Diogo Santos-Martins, Andreas Koch, Stefano Forli

Proceedings of the 28th Euromicro International Conference on Parallel, 2020

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, Stefano Forli, Oscar R. Hernandez, Jeremy C. Smith, Ada Sedova

Proceedings of the BCB '20: 11th ACM International Conference on Bioinformatics, 2020

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, Stefano Forli

J. Comput. Aided Mol. Des., 2019

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, Stefano Forli, David L. Mobley

J. Comput. Aided Mol. Des., 2019

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

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

2014

AutoDock4_Zn: 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

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