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Updated: Nov 23, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Proteochemometrics - recent developments in bioactivity and selectivity modeling
Brandon J Bongers1, Adriaan P IJzerman1, Gerard J P Van Westen1
1Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands.
Abstract:
Proteochemometrics is a machine learning based modeling approach relying on a combination of ligand and protein descriptors. With ongoing developments in machine learning and increases in public data the technique is more frequently applied in early drug discovery, typically in ligand-target binding prediction. Common applications include improvements to single target quantitative structure-activity relationship models, protein selectivity and promiscuity modeling, and large-scale deep learning approaches. The increase in predictive power using proteochemometrics is observed in multi-target bioactivity modeling, opening the door to more extensive studies covering whole protein families. On top of that, with deep learning fueling more complex and larger scale models, proteochemometrics allows faster and higher quality computational models supporting the design, make, test cycle.
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