vScreenML v2.0: Improved Machine Learning Classification for Reducing False Positives in Structure-Based Virtual Screening
Year: 2024
Type: article
Abstract: The 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. The 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 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.
Language: English
Subfield: Computational Theory and Mathematics
Field: Computer Science
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $3,296
Awards: G1226197942, G1453181110, G1518351070, G156276794, G1595757351, G1732709109, G1742171491, Track 4: Advanced CI Coordination Ecosystem: Monitoring and Measurement Services, G2114340465, G2790447815, G34258105, G3562386289, XSEDE 2.0: Integrating, Enabling and Enhancing National Cyberinfrastructure with Expanding Community Involvement, G4010157413, G4090037298, G4275568664, G4278720992, G4676131719, ACO: An Open CI Ecosystem to Advance Scientific Discovery (OpenCI), G4828753475, G5019522989, Track 3: COre National Ecosystem for CyberinfrasTructure (CONECT), G5097243881, G5148426894, G5156331529, G5221320154, G5367127336, G5386388058, G5464919783, G560129009, G6056929667, G6214533599, G63540804, G6926000687, G7197722396, G7526614437, G7772160006, G7797653384, G7918912957, G8252281214, G8286725533, Track 2: Customized Multi-tier Assistance, Training, and Computational Help (MATCH) for End User ACCESS to CI, G8372553500, G8451021191, G8499740153, G8684305011, G9000136449
OpenAlex ID: W4404489328