ArticleJournal of immunology (Baltimore, Md. : 1950)2017
Accurate Structure Prediction of CDR H3 Loops Enabled by a Novel Structure-Based C-Terminal Constraint.
Article in Journal of immunology (Baltimore, Md. : 1950), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 52 citations in OpenAlex.
- AI-Driven Design Platforms of Next-Generation Antibody Therapeutics.Topics in current chemistry (Cham) · 2026Review
- Combining computational modeling and experimental library screening to affinity-mature VEEV-neutralizing antibody F5.Protein science : a publication of the Protein Society · 2025Article
- A comprehensive overview of recent advances in generative models for antibodies.Computational and structural biotechnology journal · 2024Review
- Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens.Journal of chemical theory and computation · 2023Review
- Structural Classification of CDR-H3 in Single-Domain VMethods in molecular biology (Clifton, N.J.) · 2023Article
- A novel Fc-enhanced humanized monoclonal antibody targeting B7-H3 suppresses the growth of ESCC.Oncoimmunology · 2023Article
- Polyreactivity of antibodies from different B-cell subpopulations is determined by distinct sequence patterns of variable region.Frontiers in immunology · 2023Article
- Antigen binding by conformational selection in near-germline antibodies.The Journal of biological chemistry · 2022Article
- Antibody structure prediction using interpretable deep learning.Patterns (New York, N.Y.) · 2022Article
- NanoNet: Rapid and accurate end-to-end nanobody modeling by deep learning.Frontiers in immunology · 2022Article
- Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks.Nature communications · 2021Article
- A high-affinity human TCR-like antibody detects celiac disease gluten peptide-MHC complexes and inhibits T cell activation.Science immunology · 2021Article
- Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design.Biochemistry · 2021Review
- Interaction of clinical-stage antibodies with heme predicts their physiochemical and binding qualities.Communications biology · 2021Article
- Conformational Ensembles of Antibodies Determine Their Hydrophobicity.Biophysical journal · 2021Article
- Robustification of RosettaAntibody and Rosetta SnugDock.PloS one · 2021Article
- Macromolecular modeling and design in Rosetta: recent methods and frameworks.Nature methods · 2020Review
- Geometric potentials from deep learning improve prediction of CDR H3 loop structures.Bioinformatics (Oxford, England) · 2020Article
- Plasma Cells Are the Most Abundant Gluten Peptide MHC-expressing Cells in Inflamed Intestinal Tissues From Patients With Celiac Disease.Gastroenterology · 2019Article
- Development of a novel anti-HER2 scFv by ribosome display and in silico evaluation of its 3D structure and interaction with HER2, alone and after fusion to LAMP2B.Molecular biology reports · 2018Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Ab structure prediction has made great strides, but accurately modeling CDR H3 loops remains elusive. Unlike the other five CDR loops, CDR H3 does not adopt canonical conformations and must be modeled de novo. During Antibody Modeling Assessment II, we found that biasing simulations toward kinked conformations enables generating low-root mean square deviation models (Weitzner et al. 2014. Proteins 82: 1611-1623), and since then, we have presented new geometric parameters defining the kink conformation (Weitzner et al. 2015. Structure 23: 302-311). In this study, we use these parameters to develop a new biasing constraint. When applied to a benchmark set of high-quality CDR H3 loops, the average minimum root mean square deviation sampled is 0.93 Å, compared with 1.34 Å without the constraint. We then test the performance of the constrained de novo method for homology modeling and rigid-body docking and present the results for 1) the Antibody Modeling Assessment II targets, 2) the 2009 RosettaAntibody benchmark set, and 3) the high-quality set.
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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.