Molecular docking scripts for virtual screening studies

SerenaRosi's GitHub page

Reproducing paper: "Benchmarking the Performance of Irregular Computations in AutoDock-GPU Molecular Docking"

This package facilitates molecular docking simulations aimed at analyzing interactions between a target biological system and a collection of potential drug molecules. By leveraging computational algorithms, it ranks these molecules based on docking scores and interaction energies, providing insights into their suitability as drug candidates.

Python utility that bulk-submits receptor/ligand pairs to the HDOCK server, tracks job tokens

Dok2any is a small Python package designed to convert dok files generated by LeDock molecular docking software, a non-standard chemical structure file format unique for LeDock, to various other chemical structure formats using Openbabel.

Reproducing IA^3 2021 paper: "Mapping Irregular Computations for Molecular Docking to the SX-Aurora TSUBASA Vector Engine"

AffiniPy: Automated Molecular Docking and Scoring Pipeline Prototype. End-to-end virtual screening in Python integrating RDKit, Dimorphite-DL, Meeko, pdb2pqr, AutoDock Vina, and MDAnalysis for protein–ligand docking, descriptor profiling, and composite affinity scoring. Reproducible. Parallelized. Plug-and-play.

Reproducing IA^3 2020 Paper: "Parallelizing Irregular Computations for Molecular Docking"

In-house Python code to assist for BIOS competition