Diogo Santos-Martins

17 papers C 1Journal 13Unranked 3

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	Architecting Tensor Core-Based Reductions for Irregular Molecular Docking Kernels. SC Workshops Leonardo Solis-Vasquez, Andreas F. Tillack, Diogo Santos-Martins, Andreas Koch, Stefano Forli
2025	J	`jnl`	Meeko: Molecule Parametrization and Software Interoperability for Docking and Beyond. J. Chem. Inf. Model. Diogo Santos-Martins, Yiran He, Jérôme Eberhardt, Parnika Sharma, Niccolò Bruciaferri, Matthew Holcomb, Manuel A. Llanos, Althea T. Hansel-Harris, Allison Pearl Barkdull, Andreas F. Tillack, Giulia Bianco, May-Linn Paulsen, Joani Mato, Ishan Taneja, Stefano Forli
2024	J	`jnl`	CosolvKit: a Versatile Tool for Cosolvent MD Preparation and Analysis. J. Chem. Inf. Model. Niccolò Bruciaferri, Jérôme Eberhardt, Manuel A. Llanos, Johannes R. Loeffler, Matthew Holcomb, Monica L. Fernández-Quintero, Diogo Santos-Martins, Andrew B. Ward, Stefano Forli
2023	J	`jnl`	Reactive Docking: A Computational Method for High-Throughput Virtual Screenings of Reactive Species. J. Chem. Inf. Model. Giulia Bianco, Matthew Holcomb, Diogo Santos-Martins, Andreas F. Tillack, Althea T. Hansel-Harris, Stefano Forli
2023	J	`jnl`	Ringtail: A Python Tool for Efficient Management and Storage of Virtual Screening Results. J. Chem. Inf. Model. Althea T. Hansel-Harris, Diogo Santos-Martins, Niccolò Bruciaferri, Andreas F. Tillack, Matthew Holcomb, Stefano Forli
2022	J	`jnl`	Benchmarking the performance of irregular computations in AutoDock-GPU molecular docking. Parallel Comput. Leonardo Solis-Vasquez, Andreas F. Tillack, Diogo Santos-Martins, Andreas Koch, Scott LeGrand, Stefano Forli
2021	J	`jnl`	AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. J. Chem. Inf. Model. Jérôme Eberhardt, Diogo Santos-Martins, Andreas F. Tillack, Stefano Forli
2020	C	`conf`	Evaluating the Energy Efficiency of OpenCL-accelerated AutoDock Molecular Docking. PDP Leonardo Solis-Vasquez, Diogo Santos-Martins, Andreas Koch, Stefano Forli
2020	—	`conf`	GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research. BCB 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
2020	—	`conf`	Parallelizing Irregular Computations for Molecular Docking. IA3@SC Leonardo Solis-Vasquez, Diogo Santos-Martins, Andreas F. Tillack, Andreas Koch, Jérôme Eberhardt, Stefano Forli
2020	J	`jnl`	Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. J. Chem. Inf. Model. 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
2019	J	`jnl`	Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4. J. Comput. Aided Mol. Des. 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
2019	J	`jnl`	D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU. J. Comput. Aided Mol. Des. Diogo Santos-Martins, Jérôme Eberhardt, Giulia Bianco, Leonardo Solis-Vasquez, Francesca Alessandra Ambrosio, Andreas Koch, Stefano Forli
2016	J	`jnl`	Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas. J. Comput. Aided Mol. Des. Diogo Santos-Martins, Pedro Alexandrino Fernandes, Maria João Ramos
2016	J	`jnl`	Interaction with specific HSP90 residues as a scoring function: validation in the D3R Grand Challenge 2015. J. Comput. Aided Mol. Des. Diogo Santos-Martins
2014	J	`jnl`	AutoDock4 J. Chem. Inf. Model. Diogo Santos-Martins, Stefano Forli, Maria João Ramos, Arthur J. Olson
2014	J	`jnl`	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. J. Comput. Aided Mol. Des. Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Diogo Santos-Martins, Arthur J. Olson