NetSolP: predicting protein solubility in Escherichia coli using language models

Abstract Motivation Solubility and expression levels of proteins can be a limiting factor for large-scale studies and industrial production. By determining the solubility and expression directly from the protein sequence, the success rate of wet-lab experiments can be increased. Results In this stud...

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Bibliographic Details
Published in:Bioinformatics 2022-01, Vol.38 (4), p.941-946
Main Authors: Thumuluri, Vineet, Martiny, Hannah-Marie, Almagro Armenteros, Jose J, Salomon, Jesper, Nielsen, Henrik, Johansen, Alexander Rosenberg
Format: Article
Language:English
Subjects:
Escherichia coli
Language
Proteins
Software
Solubility
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Summary:Abstract Motivation Solubility and expression levels of proteins can be a limiting factor for large-scale studies and industrial production. By determining the solubility and expression directly from the protein sequence, the success rate of wet-lab experiments can be increased. Results In this study, we focus on predicting the solubility and usability for purification of proteins expressed in Escherichia coli directly from the sequence. Our model NetSolP is based on deep learning protein language models called transformers and we show that it achieves state-of-the-art performance and improves extrapolation across datasets. As we find current methods are built on biased datasets, we curate existing datasets by using strict sequence-identity partitioning and ensure that there is minimal bias in the sequences. Availability and implementation The predictor and data are available at https://services.healthtech.dtu.dk/service.php?NetSolP and the open-sourced code is available at https://github.com/tvinet/NetSolP-1.0. Supplementary information Supplementary data are available at Bioinformatics online.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btab801