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.

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.

In-house Python code to assist for BIOS competition

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

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

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.