ArticleNucleic acids research2014
PASTA 2.0: an improved server for protein aggregation prediction.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 233 papers.
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233 citing papers in PubMed, 483 citations in OpenAlex.
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- Assessment of Aggregation- and Condensation-Prone Regions of Proteins Involved in Neurodegenerative, Neurological and Mental-State Diseases.Biomolecules · 2026Article
- Bioinformatic assessment of the potential amyloidogenicity of the human and evolutionarily more ancient proteomes.The Biochemical journal · 2026Article
- Charged membrane interfaces reshape the nucleation landscape of RIPK3 amyloid variants.European biophysics journal : EBJ · 2026Article
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- 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
- Matrix plasticity and the molecular basis of extracellular filament assembly inScience advances · 2026Article
- YB-1 AP-CSD Forms Cross-β Amyloid Fibrils Without Secondary-Structure Conversion In Vitro.International journal of molecular sciences · 2026Article
- Integrated Symbiotic Pleiotropy: Long Non-Coding RNAs and Disordered Proteins Interweaving the Functional Layers of the Eukaryotic Cell.International journal of molecular sciences · 2026Review
- Cross-Species Amyloid-like Features Shared by Mammalian andMicroorganisms · 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
- Degradation Determinants Are Abundant in Human Noncanonical Proteins and Minor Annotated Isoforms.Genome biology and evolution · 2026Article
- The Blobulator: A Toolkit for Identification and Visual Exploration of Hydrophobic Modularity in Protein Sequences.Journal of chemical information and modeling · 2026Article
- Assessment of the biochemical basis underlying the resistance against systemic amyloidosis.Scientific reports · 2026Article
- Antimicrobial Peptides as Cross-Seeding Modulators at the Neurodegenerative-Infectious Interface.Research (Washington, D.C.) · 2026Review
- Rational discovery of peptide inhibitors targeting Keap1: a focus on neurodegenerative diseases.Frontiers in bioinformatics · 2026Article
173 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The formation of amyloid aggregates upon protein misfolding is related to several devastating degenerative diseases. The propensities of different protein sequences to aggregate into amyloids, how they are enhanced by pathogenic mutations, the presence of aggregation hot spots stabilizing pathological interactions, the establishing of cross-amyloid interactions between co-aggregating proteins, all rely at the molecular level on the stability of the amyloid cross-beta structure. Our redesigned server, PASTA 2.0, provides a versatile platform where all of these different features can be easily predicted on a genomic scale given input sequences. The server provides other pieces of information, such as intrinsic disorder and secondary structure predictions, that complement the aggregation data. The PASTA 2.0 energy function evaluates the stability of putative cross-beta pairings between different sequence stretches. It was re-derived on a larger dataset of globular protein domains. The resulting algorithm was benchmarked on comprehensive peptide and protein test sets, leading to improved, state-of-the-art results with more amyloid forming regions correctly detected at high specificity. The PASTA 2.0 server can be accessed at http://protein.bio.unipd.it/pasta2/.
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Registered trials
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.