ArticlePloS one2015
Prediction of Spontaneous Protein Deamidation from Sequence-Derived Secondary Structure and Intrinsic Disorder.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A systematic review of recent trends in research on therapeutically significant L-asparaginase and acute lymphoblastic leukemia.Molecular biology reports · 2022Pooled it
- Accurate prediction of asparagine deamidation in biologics using advanced machine learning models.Briefings in bioinformatics · 2026Article
- Mechanism-Driven Features Enable Asn Deamidation Reactivity Prediction via Machine Learning Methods.Journal of chemical information and modeling · 2025Article
- Unveiling the Accurate Site-SpecificAnalytical chemistry · 2025Article
- Advances in the Study of Protein Deamidation: Unveiling Its Influence on Aging, Disease Progression, Forensics and Therapeutic Efficacy.Proteomes · 2025Review
- The Accurate Prediction of Antibody Deamidations by Combining High-Throughput Automated Peptide Mapping and Protein Language Model-Based Deep Learning.Antibodies (Basel, Switzerland) · 2024Article
- Veneer Is a Webtool for Rapid, Standardized, and Transparent Interpretation, Annotation, and Reporting of Mammalian Cell SurfaceJournal of proteome research · 2024Article
- Heat-induced structural and chemical changes to a computationally designed miniprotein.Protein science : a publication of the Protein Society · 2024Article
- TDP-43 proteinopathy in ALS is triggered by loss of ASRGL1 and associated with HML-2 expression.Nature communications · 2024Article
- Mobile Affinity Selection Chromatography Analysis of Therapeutic Monoclonal Antibodies.Analytical chemistry · 2023Article
- Conformational Control of Fast Asparagine Deamidation in a Norovirus Capsid Protein.Biochemistry · 2023Article
- In Silico Prediction Method for Protein Asparagine Deamidation.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Mechanisms of Deamidation of Asparagine Residues and Effects of Main-Chain Conformation on Activation Energy.International journal of molecular sciences · 2020Article
- Machine Learning Enables Accurate Prediction of Asparagine Deamidation Probability and Rate.Molecular therapy. Methods & clinical development · 2019Article
- Improved Electrophoretic Separation to Assist the Monitoring of Bcl-xL Post-Translational Modifications.International journal of molecular sciences · 2019Article
- Protein asparagine deamidation prediction based on structures with machine learning methods.PloS one · 2017Article
- Article
- Deciphering deamidation and isomerization in therapeutic proteins: Effect of neighboring residue.mAbsArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Asparagine residues in proteins undergo spontaneous deamidation, a post-translational modification that may act as a molecular clock for the regulation of protein function and turnover. Asparagine deamidation is modulated by protein local sequence, secondary structure and hydrogen bonding. We present NGOME, an algorithm able to predict non-enzymatic deamidation of internal asparagine residues in proteins in the absence of structural data, using sequence-based predictions of secondary structure and intrinsic disorder. Compared to previous algorithms, NGOME does not require three-dimensional structures yet yields better predictions than available sequence-only methods. Four case studies of specific proteins show how NGOME may help the user identify deamidation-prone asparagine residues, often related to protein gain of function, protein degradation or protein misfolding in pathological processes. A fifth case study applies NGOME at a proteomic scale and unveils a correlation between asparagine deamidation and protein degradation in yeast. NGOME is freely available as a webserver at the National EMBnet node Argentina, URL: http://www.embnet.qb.fcen.uba.ar/ in the subpage "Protein and nucleic acid structure and sequence analysis".
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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.