ArticleNucleic acids research2015
AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 116 papers.
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Who cites it
116 citing papers in PubMed.
- Polar vs Non-polar Excipients in BSA Aggregation.Pharmaceutical research · 2026Article
- Engineering of a Carbonic Anhydrase fromInternational journal of molecular sciences · 2026Article
- MAVISp: A modular structure-based framework for protein variant effects.Protein science : a publication of the Protein Society · 2026Article
- Experimentally validated deep learning control of protein aggregation.Communications chemistry · 2026Article
- Hotspot Interactions between Two Fab Molecules in Molecular Dynamics Simulations Improve Predictive Models of Aggregation Kinetics.Molecular pharmaceutics · 2026Article
- AGGRESCAN and its evolution: A two-decade perspective on protein aggregation prediction.Biophysical reviews · 2026Review
- Engineering mammalian protein secretion: Toward the convergence of high-throughput biology and computational methods.Cell systems · 2025Review
- Investigating Local Sequence-Structural Attributes of Amyloidogenic Light Chain Variable Domains.Proteins · 2025Article
- Aggregation-Prone Pathogenic SOD1 Variants in Amyotrophic Lateral Sclerosis: Insights from Computational Genomics and Evolutionary Conservation.Journal of molecular neuroscience : MN · 2025Article
- Prediction of aggregation in monoclonal antibodies from molecular surface curvature.Scientific reports · 2025Article
- Enhancing the Protein Stability of an Anticancer VHH-Fc Heavy Chain Antibody through Computational Modeling and Variant Design.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- 1000 fold Ultra-Photosensitized Fluorescent Protein Mimics Toward Photocatalytic Proximity Labeling and Proteomic Profiling Functions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- AI-augmented physics-based docking for antibody-antigen complex prediction.Bioinformatics (Oxford, England) · 2025Article
- Learning the rules of peptide self-assembly through data mining with large language models.Science advances · 2025Article
- AggNet: Advancing protein aggregation analysis through deep learning and protein language model.Protein science : a publication of the Protein Society · 2025Article
- A Practical Guide to Computational Tools for Engineering Biocatalytic Properties.International journal of molecular sciences · 2025Review
- Article
- Advanced glycation end-products accelerate amyloid deposits in adipocyte's lipid droplets.Cell death & disease · 2024Article
- Molecular Dynamics Simulations Reveal How Competing Protein-Surface Interactions for Glycine, Citrate, and Water Modulate Stability in Antibody Fragment Formulations.Molecular pharmaceutics · 2024Article
- Predictive Model Building for Aggregation Kinetics Based on Molecular Dynamics Simulations of an Antibody Fragment.Molecular pharmaceutics · 2024Article
56 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein aggregation underlies an increasing number of disorders and constitutes a major bottleneck in the development of therapeutic proteins. Our present understanding on the molecular determinants of protein aggregation has crystalized in a series of predictive algorithms to identify aggregation-prone sites. A majority of these methods rely only on sequence. Therefore, they find difficulties to predict the aggregation properties of folded globular proteins, where aggregation-prone sites are often not contiguous in sequence or buried inside the native structure. The AGGRESCAN3D (A3D) server overcomes these limitations by taking into account the protein structure and the experimental aggregation propensity scale from the well-established AGGRESCAN method. Using the A3D server, the identified aggregation-prone residues can be virtually mutated to design variants with increased solubility, or to test the impact of pathogenic mutations. Additionally, A3D server enables to take into account the dynamic fluctuations of protein structure in solution, which may influence aggregation propensity. This is possible in A3D Dynamic Mode that exploits the CABS-flex approach for the fast simulations of flexibility of globular proteins. The A3D server can be accessed at http://biocomp.chem.uw.edu.pl/A3D/.
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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.