vScreenML v2.0: Improved Machine Learning Classification for Reducing False Positives in Structure-Based Virtual Screening

Enthusiastic adoption of make-on-demand chemical libraries for virtual screening has highlighted the need for methods that deliver improved hit-finding discovery rates. Traditional virtual screening methods are often inaccurate, with most compounds nominated in a virtual screen not engaging the intended target protein to any detectable extent. Emerging machine learning approaches have made significant progress in this regard, including our previously-described tool vScreenML. Broad adoption of vScreenML was hindered by its challenging usability and dependencies on certain obsolete or proprietary software packages. Here, we introduce vScreenML 2.0 (https://github.com/gandrianov/vScreenML2) to address each of these limitations with a streamlined Python implementation. Through careful benchmarks, we show that vScreenML 2.0 outperforms other widely-used tools for virtual screening hit discovery.