ArticleNucleic acids research2017
SODA: prediction of protein solubility from disorder and aggregation propensity.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Assessment of Aggregation- and Condensation-Prone Regions of Proteins Involved in Neurodegenerative, Neurological and Mental-State Diseases.Biomolecules · 2026Article
- Persistent sheaf Laplacian analysis of protein stability and solubility changes upon mutation.Protein science : a publication of the Protein Society · 2026Article
- Strategies for enhancing protein solubility: methods, applications, and prospects.NPJ science of food · 2026Review
- Harnessing deep learning to accelerate the development of antibodies and aptamers.Acta pharmaceutica Sinica. B · 2026Review
- First report of novel single-nucleotide polymorphisms and genetic characteristics in the open reading frame of the prion protein gene (Frontiers in veterinary science · 2026Article
- Novel polymorphisms and functional characterization of the prion protein gene in sparrows (Frontiers in veterinary science · 2026Article
- Insights into Caspase-6 Mutations and Neuropathology in Huntington's Disease and Psychiatric Disorders: A Structural Genomics and Drug Repurposing Approach.Molecular neurobiology · 2025Article
- Article
- Aggregation-Prone Pathogenic SOD1 Variants in Amyotrophic Lateral Sclerosis: Insights from Computational Genomics and Evolutionary Conservation.Journal of molecular neuroscience : MN · 2025Article
- SOuLMuSiC, a novel tool for predicting the impact of mutations on protein solubility.Scientific reports · 2025Article
- Computational Identification and Functional Analysis of Potentially Pathogenic nsSNPs in the NLRP3 Gene Linked to Alzheimer's Disease.Cell biochemistry and biophysics · 2025Article
- First description of novel compound heterozygous mutations in HYCC1: clinical evaluations and molecular analysis in patient with hypomyelinating leukodystrophy-5 with retrospective view.Journal of human genetics · 2025Article
- A Practical Guide to Computational Tools for Engineering Biocatalytic Properties.International journal of molecular sciences · 2025Review
- Insight into Protein Engineering: FromCurrent pharmaceutical design · 2025Review
- Article
- A structural genomics approach to investigate Dystrophin mutations and their impact on the molecular pathways of Duchenne muscular dystrophy.Frontiers in genetics · 2025Article
- Novel Single-Nucleotide Polymorphisms (SNPs) and Genetic Studies of the Shadow of Prion Protein (Animals : an open access journal from MDPI · 2024Article
- Elucidating the Impact of Deleterious Mutations on IGHG1 and Their Association with Huntington's Disease.Journal of personalized medicine · 2024Article
- Integration of persistent Laplacian and pre-trained transformer for protein solubility changes upon mutation.Computers in biology and medicine · 2024Article
- Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Solubility is an important, albeit not well understood, feature determining protein behavior. It is of paramount importance in protein engineering, where similar folded proteins may behave in very different ways in solution. Here we present SODA, a novel method to predict the changes of protein solubility based on several physico-chemical properties of the protein. SODA uses the propensity of the protein sequence to aggregate as well as intrinsic disorder, plus hydrophobicity and secondary structure preferences to estimate changes in solubility. It has been trained and benchmarked on two different datasets. The comparison to other recently published methods shows that SODA has state-of-the-art performance and is particularly well suited to predict mutations decreasing solubility. The method is fast, returning results for single mutations in seconds. A usage example estimating the full repertoire of mutations for a human germline antibody highlights several solubility hotspots on the surface. The web server, complete with RESTful interface and extensive help, can be accessed from URL: http://protein.bio.unipd.it/soda.
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