MD for Affinity Prediction

Repository used to generate the data used in the paper [1]. Complexes from the pdbbind v2020 dataset were used to generate data from the crystallographic structures. The molecular dynamics trajectories used to generate the data are deposited at: https://zenodo.org/records/11172815.

Usage:
Use the following scripts to generate the data:

• compute_descriptors_for_cystal_structures.py - generates data dal crystallographic complexes
• compute_descriptors_for_trajectory.py - generates data for trajactories of molecular dynamics
• compute_ligand_static_descriptors.py - generates static ligand decryptors

Requirements:

• python 3.10,
• Packages: prolif, rdkit, pandas, MDAnalysis,

References:

1. Poziemski J, Yurkevych A, Siedlecki P. Assessment of molecular dynamics time series descriptors in protein-ligand affinity prediction. ChemRxiv. 2024; doi:10.26434/chemrxiv-2024-dxv36