FAIR² DATA article
Front. Bioinform.
Sec. Integrative Bioinformatics
Volume 5 - 2025 | doi: 10.3389/fbinf.2025.1634111
This article is part of the Research TopicAI in Integrative BioinformaticsView all articles
Structure-Based Prediction of SARS-CoV-2 Variant Properties Using Machine Learning on Mutational Neighborhoods
Provisionally accepted
- 1Universiteit Leiden Leiden Academic Centre for Drug Research, Leiden, Netherlands
- 2Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- 3GO FAIR Foundation, Leiden, Netherlands
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This dataset presents a structure-enriched resource of theoretical and empirical SARS-CoV-2 spike-receptor-binding-domain (RBD) variants, developed under the STAYAHEAD project for pandemic preparedness. It integrates large-scale in silico structure predictions with empirical biophysical measurements. The dataset includes 3,705 single-point Wuhan-Hu-1 RBD variants and 100 higherorder Omicron BA.1/BA.2 variants, annotated with AlphaFold2 and ESMFold metrics and Bio2Byte sequence-based predictors. Structural descriptors-RMSD, TM-score, plDDT, solvent accessibility, hydrophobicity, aggregation propensity-are linked to ACE2 binding and expression data from deep mutational scanning. Provided as a FAIR² Data Package, it supports structure-function analysis, variant modeling, and responsible reuse in virology, structural biology, and computational protein science.
Keywords: SARS-CoV-2, Spike protein, Receptor-binding domain (RBD), protein structure prediction, AlphaFold2, ESMFold, deep mutational scanning, Variant of Concern (VOC)
Received: 23 May 2025; Accepted: 24 Jul 2025.
Copyright: © 2025 Van Den Boom, Schultes and Hankemeier. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Erik Schultes, Universiteit Leiden Leiden Academic Centre for Drug Research, Leiden, Netherlands
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