Enabling performance portability on the LiGen drug discovery pipeline
Sep 1, 2024
ZSMILES: An Approach for Efficient SMILES Storage for Random Access in Virtual Screening
Jul 1, 2024
LIGATE - LIgand Generator and portable drug discovery platform AT Exascale
Jul 1, 2024
A Portable Drug Discovery Platform for Urgent Computing
Jul 1, 2024
muDock
Molecular docking is a well-known problem in scientific literature. It aims to estimate the 3D displacement of a molecule with a small molecular weight, named ligand, when it interacts with the target protein. The main issue is the number of degree of freedom involved in the operation. Due to the difference in size between the protein and ligand, we need to find the correct position and orientation of the ligand inside a pocket cavity. Moreover, the molecules are not rigid bodies, but we can rotate a subset of their bonds, changing their geometry, without changing their chemical and physical properties. Thus, we have six degrees of freedom for rigid rototranslations in a 3D space and one additional degree of freedom for each of those bonds. Arguably, the most popular tool that performs molecular docking is autodock (https://autodock.scripps.edu/). Its implementation is composed of a feature rich ecosystem of tools, that might employ different optimization strategies to solve the exploration problem.
Jun 1, 2024
Unlocking performance portability on LUMI-G supercomputer: A virtual screening case study
Apr 1, 2024
Out of kernel tuning and optimizations for portable large-scale docking experiments on GPUs
Feb 1, 2024
Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach
Jul 4, 2023
LIGATE
The overall purpose is the automation of the drug design process, which is currently performed with substantial human effort throughout the different phases of the process: preparation of input parameters, management of data sets with billions of molecules, interaction with HPC queue management systems to handle jobs, and optimization of scoring function parameters and thresholds.
Jan 1, 2023