Complex machine learning model needs complex testing: Examining predictability of molecular binding affinity by a graph neural network.

Autor: Nikolaienko T; SoftServe, Inc., Lviv, Ukraine.; Faculty of Physics, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine., Gurbych O; Blackthorn AI Ltd., London, UK.; Department of Artificial Intelligence Systems, Lviv Polytechnic National University, Lviv, Ukraine., Druchok M; SoftServe, Inc., Lviv, Ukraine.; Institute for Condensed Matter Physics, NAS of Ukraine, Lviv, Ukraine.
Jazyk: angličtina
Zdroj: Journal of computational chemistry [J Comput Chem] 2022 Apr 15; Vol. 43 (10), pp. 728-739. Date of Electronic Publication: 2022 Feb 24.
DOI: 10.1002/jcc.26831
Abstrakt: Drug discovery pipelines typically involve high-throughput screening of large amounts of compounds in a search of potential drugs candidates. As a chemical space of small organic molecules is huge, a "navigation" over it urges for fast and lightweight computational methods, thus promoting machine-learning approaches for processing huge pools of candidates. In this contribution, we present a graph-based deep neural network for prediction of protein-drug binding affinity and assess its predictive power under thorough testing conditions. Within the suggested approach, both protein and drug molecules are represented as graphs and passed to separate graph sub-networks, then concatenated and regressed towards a binding affinity. The neural network is trained on two binding affinity datasets-PDBbind and data imported from RCSB Protein Data Bank. In order to explore the generalization capabilities of the model we go beyond traditional random or leave-cluster-out techniques and demonstrate the need for more elaborate model performance assessment - six different strategies for test/train data partitioning (random, time- and property-arranged, protein- and ligand-clustered) with a k-fold cross-validation are engaged. Finally, we discuss the model performance in terms of a set of metrics for different split strategies and fold arrangement. Our code is available at https://github.com/SoftServeInc/affinity-by-GNN.
(© 2022 Wiley Periodicals LLC.)
Databáze: MEDLINE
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