ArticleNucleic acids research2024
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Bridging Generative AI and Diffusion Models With Molecular Simulation to Design Anti-Quorum-Sensing De novo Peptides Targeting LasR of Pseudomonas aeruginosa.Probiotics and antimicrobial proteins · 2026Article
- AGGRESCAN and its evolution: A two-decade perspective on protein aggregation prediction.Biophysical reviews · 2026Review
- Characterization of BRCA1-Associated Protein-1 (BAP1) Aggregation Properties Induced by Cancer-Associated Mutations.Chembiochem : a European journal of chemical biology · 2025Article
- Neurodegeneration Through the Lens of Bioinformatics Approaches: Computational Mechanisms of Protein Misfolding.International journal of molecular sciences · 2025Review
- AggNet: Advancing protein aggregation analysis through deep learning and protein language model.Protein science : a publication of the Protein Society · 2025Article
- Three scenarios for amyloid transformation in the context of the funnel model.Computational and structural biotechnology journal · 2025Article
- Article
- Aggregating amyloid resources: A comprehensive review of databases on amyloid-like aggregation.Computational and structural biotechnology journal · 2024Review
- A comprehensive overview of recent advances in generative models for antibodies.Computational and structural biotechnology journal · 2024Review
- Proteomic Evidence for Amyloidogenic Cross-Seeding in Fibrinaloid Microclots.International journal of molecular sciences · 2024Article
- Aggrescan4D: A comprehensive tool for pH-dependent analysis and engineering of protein aggregation propensity.Protein science : a publication of the Protein Society · 2024Review
- Exploring protein functions from structural flexibility using CABS-flex modeling.Protein science : a publication of the Protein Society · 2024Review
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Authors and funding
9 authors.
Funding
Abstract
Protein aggregation is behind the genesis of incurable diseases and imposes constraints on drug discovery and the industrial production and formulation of proteins. Over the years, we have been advancing the Aggresscan3D (A3D) method, aiming to deepen our comprehension of protein aggregation and assist the engineering of protein solubility. Since its inception, A3D has become one of the most popular structure-based aggregation predictors because of its performance, modular functionalities, RESTful service for extensive screenings, and intuitive user interface. Building on this foundation, we introduce Aggrescan4D (A4D), significantly extending A3D's functionality. A4D is aimed at predicting the pH-dependent aggregation of protein structures, and features an evolutionary-informed automatic mutation protocol to engineer protein solubility without compromising structure and stability. It also integrates precalculated results for the nearly 500,000 jobs in the A3D Model Organisms Database and structure retrieval from the AlphaFold database. Globally, A4D constitutes a comprehensive tool for understanding, predicting, and designing solutions for specific protein aggregation challenges. The A4D web server and extensive documentation are available at https://biocomp.chem.uw.edu.pl/a4d/. This website is free and open to all users without a login requirement.
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Registered trials
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