ArticlePLoS computational biology2022
Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 15 citations in OpenAlex.
- How new approach methods are reshaping virology research.Journal of virology · 2026Review
- Africa is an Essential Partner in the Research and Development of an HIV Vaccine.Current HIV research · 2026Review
- Advances in linear epitope-based subunit vaccines powered by artificial intelligence: current status and challenges.Frontiers in immunology · 2026Review
- What does AlphaFold3 learn about antibody and nanobody docking, and what remains unsolved?mAbs · 2025Article
- Retrospective SARS-CoV-2 human antibody development trajectories are largely sparse and permissive.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Phenomenological Modeling of Antibody Response from Vaccine Strain Composition.Antibodies (Basel, Switzerland) · 2025Article
- A paradigm shift in simulating affinity maturation to elicit broadly neutralizing antibodies.Frontiers in immunology · 2025Review
- Common framework mutations impact antibody interfacial dynamics and flexibility.Frontiers in immunology · 2023Article
- Prediction of antibody binding to SARS-CoV-2 RBDs.Bioinformatics advances · 2023Article
- On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations.Antibodies (Basel, Switzerland) · 2022Article
- Moving the needle: Employing deep reinforcement learning to push the boundaries of coarse-grained vaccine models.Frontiers in immunology · 2022Article
- A Coarse-Grained Model of Affinity Maturation Indicates the Importance of B-Cell Receptor Avidity in Epitope Subdominance.Frontiers in immunology · 2022Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The design of vaccines against highly mutable pathogens, such as HIV and influenza, requires a detailed understanding of how the adaptive immune system responds to encountering multiple variant antigens (Ags). Here, we describe a multiscale model of B cell receptor (BCR) affinity maturation that employs actual BCR nucleotide sequences and treats BCR/Ag interactions in atomistic detail. We apply the model to simulate the maturation of a broadly neutralizing Ab (bnAb) against HIV. Starting from a germline precursor sequence of the VRC01 anti-HIV Ab, we simulate BCR evolution in response to different vaccination protocols and different Ags, which were previously designed by us. The simulation results provide qualitative guidelines for future vaccine design and reveal unique insights into bnAb evolution against the CD4 binding site of HIV. Our model makes possible direct comparisons of simulated BCR populations with results of deep sequencing data, which will be explored in future applications.
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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.