Dataset Information

Solubility-Weighted Index: fast and accurate prediction of protein solubility.

ABSTRACT:

Motivation

Recombinant protein production is a widely used technique in the biotechnology and biomedical industries, yet only a quarter of target proteins are soluble and can therefore be purified.

Results

We have discovered that global structural flexibility, which can be modeled by normalized B-factors, accurately predicts the solubility of 12?216 recombinant proteins expressed in Escherichia coli. We have optimized these B-factors, and derived a new set of values for solubility scoring that further improves prediction accuracy. We call this new predictor the 'Solubility-Weighted Index' (SWI). Importantly, SWI outperforms many existing protein solubility prediction tools. Furthermore, we have developed 'SoDoPE' (Soluble Domain for Protein Expression), a web interface that allows users to choose a protein region of interest for predicting and maximizing both protein expression and solubility.

Availability and implementation

The SoDoPE web server and source code are freely available at https://tisigner.com/sodope and https://github.com/Gardner-BinfLab/TISIGNER-ReactJS, respectively. The code and data for reproducing our analysis can be found at https://github.com/Gardner-BinfLab/SoDoPE_paper_2020.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Bhandari BK

PROVIDER: S-EPMC7750957 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Publications

Solubility-Weighted Index: fast and accurate prediction of protein solubility.

Bhandari Bikash K BK Gardner Paul P PP Lim Chun Shen CS

Bioinformatics (Oxford, England) 20200901 18

<h4>Motivation</h4>Recombinant protein production is a widely used technique in the biotechnology and biomedical industries, yet only a quarter of target proteins are soluble and can therefore be purified.<h4>Results</h4>We have discovered that global structural flexibility, which can be modeled by normalized B-factors, accurately predicts the solubility of 12 216 recombinant proteins expressed in Escherichia coli. We have optimized these B-factors, and derived a new set of values for solubility ...[more]

PMID: 32559287

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Dataset Information

Solubility-Weighted Index: fast and accurate prediction of protein solubility.

Motivation

Results

Availability and implementation

Supplementary information

Publications

Solubility-Weighted Index: fast and accurate prediction of protein solubility.

Similar Datasets

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