The euroSAMPL1 p<i>K</i><sub>a</sub> blind prediction and reproducible research data management challenge

The development and testing of methods in computational chemistry for the prediction of physicochemical properties is by now a mature form of scientific research, with a number of different methods ranging from molecular mechanics simulations, over quantum calculations, to empirical and machine learning models. Blind prediction challenges for these properties are regularly organized to allow researchers from academia and industry to test their methods in a fair and unbiased manner. At the same time, research data management (RDM) is still not utilized as extensively as it could be in the development and application of such models, especially in academia. In particular, the FAIR standards (Findable, Accessible, Interoperable, Reusable) can serve as guidelines for good RDM, but many models, the data used to train them, and the data they generate fall short of one, or multiple, of these standards. The goal of the first euroSAMPL p<i>K</i><sub>a</sub> blind prediction challenge was to promote and help develop good RDM standards for computational chemistry. To achieve this, the challenge was designed to rank not just the predictive performance of the models but also evaluate the adherence to the FAIR principles by cross-evaluation of the participants themselves. We here present the analysis of the blind prediction quality by their statistical metrics as well as of the cross-evaluation by a newly defined "FAIRscore". The results suggest that multiple methods can predict the p<i>K</i><sub>a</sub> to within chemical accuracy, but also that "consensus" predictions constructed from multiple, independent methods may outperform each individual prediction. Furthermore, the state of research data management in the field of computational chemistry is discussed, and suggestions for future improvements developed.

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Publication Details

Journal
Physical Chemistry Chemical Physics
Published
2025-01-01
DOI
https://doi.org/10.1039/d5cp01448d
Citations
2
Primary Topic
Scientific Computing and Data Management
Type
article
Field-Weighted Citation Impact
8.34

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The euroSAMPL1 pKa blind prediction and reproducible research data management challenge

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2 citations
Physical Chemistry Chemical Physics
Scientific Computing and Data Management
8.34
article

The euroSAMPL1 pKa blind prediction and reproducible research data management challenge

Björn Hein‐Janke, Nicolas Tielker, Christian Chodun, Paul Czodrowski, Juliana Gretz, Stefan M. Kast, M. H. Lim, Ricardo A. Mata, Patrick Kibies
article en
2 citations

Abstract

The development and testing of methods in computational chemistry for the prediction of physicochemical properties is by now a mature form of scientific research, with a number of different methods ranging from molecular mechanics simulations, over quantum calculations, to empirical and machine learning models. Blind prediction challenges for these properties are regularly organized to allow researchers from academia and industry to test their methods in a fair and unbiased manner. At the same time, research data management (RDM) is still not utilized as extensively as it could be in the development and application of such models, especially in academia. In particular, the FAIR standards (Findable, Accessible, Interoperable, Reusable) can serve as guidelines for good RDM, but many models, the data used to train them, and the data they generate fall short of one, or multiple, of these standards. The goal of the first euroSAMPL p<i>K</i><sub>a</sub> blind prediction challenge was to promote and help develop good RDM standards for computational chemistry. To achieve this, the challenge was designed to rank not just the predictive performance of the models but also evaluate the adherence to the FAIR principles by cross-evaluation of the participants themselves. We here present the analysis of the blind prediction quality by their statistical metrics as well as of the cross-evaluation by a newly defined "FAIRscore". The results suggest that multiple methods can predict the p<i>K</i><sub>a</sub> to within chemical accuracy, but also that "consensus" predictions constructed from multiple, independent methods may outperform each individual prediction. Furthermore, the state of research data management in the field of computational chemistry is discussed, and suggestions for future improvements developed.

Physical Chemistry Chemical PhysicsVol. 27(36)
Johannes Gutenberg University Mainz (DE), TU Dortmund University (DE), University of Göttingen (DE), Ruhr University Bochum (DE)
Deutsche Forschungsgemeinschaft, Technische Universität Dortmund
Openalex Percentile: Top 3%
Scientific Computing and Data Management
8.34
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