ArticleNucleic acids research2020
WALTZ-DB 2.0: an updated database containing structural information of experimentally determined amyloid-forming peptides.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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61 citing papers in PubMed.
- An N-terminal ATTR Fibril Segment Promotes Transthyretin Amyloid Nucleation and Polymorphism.bioRxiv : the preprint server for biology · 2026Article
- TAF15 amyloids propagate via defined motifs in a prion-like fashion.Nature communications · 2026Article
- amyloid-predict and LLPS-predict: Predicting phase separation propensities in the intrinsically disordered proteome.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Predicting Peptide Aggregation with Protein Language Model Embeddings.Journal of chemical information and modeling · 2026Article
- Experimentally validated deep learning control of protein aggregation.Communications chemistry · 2026Article
- Structural polymorphism of ex-vivo ALECT2 amyloid fibrils revealed by cryo-EM.Nature communications · 2026Article
- AGGRESCAN and its evolution: A two-decade perspective on protein aggregation prediction.Biophysical reviews · 2026Review
- PLM-eXplain: divide and conquer the protein embedding space.Bioinformatics (Oxford, England) · 2026Article
- Antimicrobial Peptides as Cross-Seeding Modulators at the Neurodegenerative-Infectious Interface.Research (Washington, D.C.) · 2026Review
- Energetic profiling reveals thermodynamic principles underlying amyloid fibril maturation.Nature communications · 2025Article
- Neurodegeneration Through the Lens of Bioinformatics Approaches: Computational Mechanisms of Protein Misfolding.International journal of molecular sciences · 2025Review
- Global Analysis of Aggregation Determinants in Small Protein Domains.bioRxiv : the preprint server for biology · 2025Article
- Navigating Homogeneous Graph Paths Through Amyloidogenic and Non-Amyloidogenic Hexapeptides.Journal of computational chemistry · 2025Article
- Substitution of tyrosine with electron-deficient aromatic amino acids improves Ac-PHF6 self-assembly and hydrogelation.RSC advances · 2025Article
- iAmyP: A Multi-view Learning for Amyloidogenic Hexapeptides Identification Based on Sequence Least Squares Programming.Interdisciplinary sciences, computational life sciences · 2025Article
- Massive experimental quantification allows interpretable deep learning of protein aggregation.Science advances · 2025Article
- AggNet: Advancing protein aggregation analysis through deep learning and protein language model.Protein science : a publication of the Protein Society · 2025Article
- Prediction and Evaluation of Protein Aggregation with Computational Methods.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Aggregating amyloid resources: A comprehensive review of databases on amyloid-like aggregation.Computational and structural biotechnology journal · 2024Review
- Unravelling the Complexity of Amyloid Peptide Core Interfaces.Journal of chemical information and modeling · 2024Article
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6 authors.
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Abstract
Transition of soluble proteins into insoluble amyloid fibrils is driven by self-propagating short sequence stretches. However, accurate prediction of aggregation determinants remains challenging. Here, we describe WALTZ-DB 2.0, an updated and significantly expanded open-access database providing information on experimentally determined amyloid-forming hexapeptide sequences (http://waltzdb.switchlab.org/). We have updated WALTZ-DB 2.0 with new entries, including: (i) experimental validation of an in-house developed dataset of 229 hexapeptides, using electron microscopy and Thioflavin-T binding assays; (ii) manual curation of 98 amyloid-forming peptides isolated from literature. Furthermore, the content has been expanded by adding novel structural information for peptide entries, including sequences of the previous version. Using a computational methodology developed in the Switch lab, we have generated 3D-models of the putative amyloid fibril cores of WALTZ-DB 2.0 entries. Structural models, coupled with information on the energetic contributions and fibril core stabilities, can be accessed through individual peptide entries. Customized filtering options for subset selections and new modelling graphical features were added to upgrade online accessibility, providing a user-friendly interface for browsing, downloading and updating. WALTZ-DB 2.0 remains the largest open-access repository for amyloid fibril formation determinants and will continue to enhance the development of new approaches focused on accurate prediction of aggregation prone sequences.
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