ArticleJournal of chemical information and modeling2021
MHCEpitopeEnergy, a Flexible Rosetta-Based Biotherapeutic Deimmunization Platform.
Article in Journal of chemical information and modeling, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
13 citing papers in PubMed.
- Molecular Survival Strategies Against Kidney Filtration: Implications for Therapeutic Protein Engineering.Biophysica · 2026Article
- Tuning ProteinMPNN to reduce protein visibility via MHC Class I through direct preference optimization.Protein engineering, design & selection : PEDS · 2025Article
- Rational engineering of minimally immunogenic nucleases for gene therapy.Nature communications · 2025Article
- A novel decoding strategy for ProteinMPNN to design with less visibility to cytotoxic T-lymphocytes.Computational and structural biotechnology journal · 2025Article
- RankMHC: Learning to Rank Class-I Peptide-MHC Structural Models.Journal of chemical information and modeling · 2024Article
- Graph-pMHC: graph neural network approach to MHC class II peptide presentation and antibody immunogenicity.Briefings in bioinformatics · 2024Article
- SpyMask enables combinatorial assembly of bispecific binders.Nature communications · 2024Article
- Accelerating therapeutic protein design with computational approaches toward the clinical stage.Computational and structural biotechnology journal · 2023Review
- Review
- Efficacy and Mechanism of Roxadustat plus Oral Iron in the Treatment of Elderly Chronic Kidney Disease with Anemia.Evidence-based complementary and alternative medicine : eCAM · 2022Article
- Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol.Frontiers in immunology · 2022Article
- Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks.Nature communications · 2021Article
- Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
As non-"self" macromolecules, biotherapeutics can trigger an immune response that can reduce drug efficacy, require patients to be taken off therapy, or even cause life-threatening reactions. To enable the flexible and facile design of protein biotherapeutics while reducing the prevalence of T-cell epitopes that drive immune recognition, we have integrated into the Rosetta protein design suite a new scoring term that allows design protocols to account for predicted or experimentally identified epitopes in the optimized objective function. This flexible scoring term can be used in any Rosetta design trajectory, can be targeted to specific regions of a protein, and can be readily extended to work with a variety of epitope predictors. By performing extensive design runs with varied design parameter choices for three case study proteins as well as a larger diverse benchmark, we show that the incorporation of this scoring term enables the effective exploration of an alternative, deimmunized sequence space to discover diverse proteins that are potentially highly deimmunized while retaining physical and chemical qualities similar to those yielded by equivalent nondeimmunizing sequence design protocols.
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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.