Controlling PyMol from afar
Published:
Do you keep downloading .pdb and .sdf files and loading them into PyMol repeatedly?
Posts
2024
Fine-tune generated molecular poses with a force field
Published:
Some molecular pose generation methods benefit from an energy relaxation post-processing step.
2023
Molecular conformation generation with a DL-based force field
Published:
Deep learning (DL) methods in structural modelling are outcompeting force fields because they overcome the two main limitations to force fields methods – the prohibitively large search space for large systems and the limited accuracy of the description of the physics1.
M. Baek and D. Baker, “Deep learning and protein structure modeling,” Nat Methods, vol. 19, no. 1, pp. 13–14, Jan. 2022, doi: 10.1038/s41592-021-01360-8. ↩
Ligands of CASF-2016
Published:
CASF-2016 is a commonly used benchmark for docking tools. Unfortunately, some of the provided ligand files cannot be loaded using RDKit (version 2022.09.1) but there is an easy remedy.
2022
Bad chemistry in old protein-ligand binding complex data set
Published:
The Astex Diverse set1 is a dataset containing the crystallized poses of 85 protein-ligand complexes. It was introduced in 2007 to address problems in previous datasets such as incorrect ligand representation.
Hartshorn, M. J. et al. Diverse, high-quality test set for the validation of protein−ligand docking performance. J. Med. Chem. 50, 726–741 (2007). ↩