Cited by 19Protein Structure and DynamicsProtein purification and stabilityMachine Learning in Bioinformatics

A3D 2.0 update for the prediction and optimization of protein solubility

Open access
Pujols, Jordi, Iglesias, Valentín, Santos, Jaime, Kuriata, Aleksander, Kmiecik, Sebastian, Ventura, Salvador·2022·Methods in molecular biology

Abstract

Protein aggregation propensity is a property imprinted in protein sequences and structures, being associated with the onset of human diseases and limiting the implementation of protein-based biotherapies. Computational approaches stand as cost-effective alternatives for reducing protein aggregation and increasing protein solubility. AGGRESCAN 3D (A3D) is a structure-based predictor of aggregation that takes into account the conformational context of a protein, aiming to identify aggregation-prone regions exposed in protein surfaces. Here we inspect the updated 2.0 version of the algorithm, which extends the application of A3D to previously inaccessible proteins and incorporates new modules to assist protein redesign. Among these features, the new server includes stability calculations and the possibility to optimize protein solubility using an experimentally validated computational pipeline. Finally, we employ defined examples to navigate the A3D RESTful service, a routine to handle extensive protein collections. Altogether, this chapter is conceived to train and assist A3D non-experts in the study of aggregation-prone regions and protein solubility redesign.

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Crossref · 10.1007/978-1-0716-1859-2_3

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Authors
Pujols, J., Iglesias, V., Santos, J., Kuriata, A., Kmiecik, S., & Ventura, S.
Affiliations
  • Universitat Autònoma de Barcelona (ES)
  • University of Warsaw (PL)
Corresponding author
Ventura, Salvador
Venue
Methods in molecular biology
Publisher
Springer US
Published
2022
Volume
2406
Pages
65-84
ISSN
  • 1064-3745 (ISSN-L)
  • 1940-6029
OpenAlex
W4226227994
Cited by
19
References
46
Citations by year
2026: 7 · 2025: 2 · 2024: 5 · 2023: 4 · 2022: 1
FWCI
5.05
Type
book chapter
Language
en
Open access
Locations
  • Methods in molecular biology (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
Funders
  • Ministerio de Economía y Competitividad (BIO2016–78,310-R)
  • Institució Catalana de Recerca i Estudis Avançats (ICREA-Academia 2015, Academia 2015)
  • Ministerio de Ciencia e Innovación (FPU17/01157, BIO2016-78310-R, FPU17)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein purification and stability
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
Keywords
protein aggregation propensity, protein solubility, aggregation-prone regions, protein redesign, protein stability prediction, REST API, computational pipeline
MeSH terms
Algorithms, Humans, Proteins, Solubility, Protein Folding, Protein Aggregates

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