ArticleBioinformatics (Oxford, England)2020
Solubility-Weighted Index: fast and accurate prediction of protein solubility.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 100 citations in OpenAlex.
- Soluble protein analog selection engine (SPASE): An automated AI-powered server to improve protein engineering workflows.Protein science : a publication of the Protein Society · 2026Article
- A Miniaturized, High-Throughput Aqueous Solvent-Centric Method for Protein Solubility Screening.Biochemistry · 2026Article
- Strategies for enhancing protein solubility: methods, applications, and prospects.NPJ science of food · 2026Review
- AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications.Science advances · 2026Article
- MiLaSol: modeling protein solubility by mixing up multiple protein language models.Bioinformatics advances · 2026Article
- Accurate de novo design of high-affinity protein-binding macrocycles using deep learning.Nature chemical biology · 2025Article
- A novel bispecific antibody targeting TNF-α and IL-6 receptor as a potent immunotherapeutic agent for inflammation.Applied microbiology and biotechnology · 2025Article
- The Achilles Heel of Protein Biochemistry: Insolubility of Recombinant Proteins-A Case Study About Producing a Rice Enzyme.International journal of molecular sciences · 2025Article
- SOuLMuSiC, a novel tool for predicting the impact of mutations on protein solubility.Scientific reports · 2025Article
- Using Large Language Model to Optimize Protein Purification: Insights from Protein Structure Literature Associated with Protein Data Bank.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- ProG-SOL: Predicting Protein Solubility Using Protein Embeddings and Dual-Graph Convolutional Networks.ACS omega · 2025Article
- An Online Server for Geometry-Aware Protein Function Annotations Through Predicted Structure.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Insight into Protein Engineering: FromCurrent pharmaceutical design · 2025Review
- GRACE: Generative Redesign in Artificial Computational Enzymology.ACS synthetic biology · 2024Article
- Prediction of Solubility of Proteins in Escherichia coli Based on Functional and Structural Features Using Machine Learning Methods.The protein journal · 2024Article
- ProSol-multi: Protein solubility prediction via amino acids multi-level correlation and discriminative distribution.Heliyon · 2024Article
- Targeting Efficient Features of Urate Oxidase to Increase Its Solubility.Applied biochemistry and biotechnology · 2024Article
- Leveraging a large language model to predict protein phase transition: A physical, multiscale, and interpretable approach.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- PLM_Sol: predicting protein solubility by benchmarking multiple protein language models with the updated Escherichia coli protein solubility dataset.Briefings in bioinformatics · 2024Article
- GPSFun: geometry-aware protein sequence function predictions with language models.Nucleic acids research · 2024Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationRecombinant 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.
resultsWe 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.