Publications

Core AutoDock-GPU

Accelerating AutoDock4 with GPUs and Gradient-Based Local Search. Diogo Santos-Martins, Leonardo Solis-Vasquez, Andreas F Tillack, Michel F Sanner, Andreas Koch, Stefano Forli. [Journal of Chemical Theory and Computation (JCTC), 2021], [ChemRxiv (preprint), 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 V. Vermaas, Rupesh Agarwal, Jeff Larkin, Duncan Poole, Diogo Santos-Martins, Leonardo Solis-Vasquez, Andreas Koch, Stefano Forli, Oscar Hernandez, Jeremy C. Smith, Ada Sedova. [11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB), 2020]
Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4. Léa El Khoury, Diogo Santos-Martins, Sukanya Sasmal, Jérôme Eberhardt, Giulia Bianco, Francesca Alessandra Ambrosio, Leonardo Solis-Vasquez, Andreas Koch, Stefano Forli, David L. Mobley. [Journal of Computer-Aided Molecular Design (JCAMD), 2019], [ChemRxiv (preprint), 2019]
D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU. Diogo Santos-Martins, Jerome Eberhardt, Giulia Bianco, Leonardo Solis-Vasquez, Francesca Alessandra Ambrosio, Andreas Koch, Stefano Forli. [Journal of Computer-Aided Molecular Design (JCAMD), 2019]

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 Computing, 2021]
Parallelizing Irregular Computations for Molecular Docking. Leonardo Solis-Vasquez, Diogo Santos-Martins, Andreas F. Tillack, Andreas Koch, Jerome Eberhardt, Stefano Forli. [10th Workshop on Irregular Applications: Architectures and Algorithms (IA3), 2020]
Evaluating the Energy Efficiency of OpenCL-accelerated AutoDock Molecular Docking. Leonardo Solis-Vasquez, Diogo Santos-Martins, Andreas Koch, Stefano Forli. [28th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), 2020]
Accelerating Molecular Docking by Parallelized Heterogeneous Computing - A Case Study of Performance, Quality of Results, and Energy-Efficiency using CPUs, GPUs, and FPGAs. Leonardo Solis-Vasquez. PhD thesis. [TUprints, 2019]

A Case Study in Using OpenCL on FPGAs: Creating an Open-Source Accelerator of the AutoDock Molecular Docking Software. Leonardo Solis-Vasquez, Andreas Koch. [5th International Workshop on FPGAs for Software Programmers (FSP), 2018]

A Performance and Energy Evaluation of OpenCL-accelerated Molecular Docking. Leonardo Solis-Vasquez, Andreas Koch. [5th International Workshop on OpenCL (IWOCL), 2017]
Molecular Docking on FPGA and GPU Platforms. I. Pechan and B. Feher. [21st International Conference on Field Programmable Logic and Applications, 2011]