AIMC Topic: Antigens
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AbEpiTope-1.0: Improved antibody target prediction by use of AlphaFold and inverse folding.
Science advances
Jun 13, 2025
B cell epitope prediction tools are crucial for designing vaccines and disease diagnostics. However, predicting which antigens a specific antibody binds to and their exact binding sites (epitopes) remains challenging. Here, we present AbEpiTope-1.0, ...
DeepInterAware: Deep Interaction Interface-Aware Network for Improving Antigen-Antibody Interaction Prediction from Sequence Data.
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Feb 11, 2025
Identifying interactions between candidate antibodies and target antigens is a key step in developing effective human therapeutics. The antigen-antibody interaction (AAI) occurs at the structural level, but the limited structure data poses a signific...
Prediction of antibody-antigen interaction based on backbone aware with invariant point attention.
BMC bioinformatics
Nov 6, 2024
BACKGROUND: Antibodies play a crucial role in disease treatment, leveraging their ability to selectively interact with the specific antigen. However, screening antibody gene sequences for target antigens via biological experiments is extremely time-c...
ANTIPASTI: Interpretable prediction of antibody binding affinity exploiting normal modes and deep learning.
Structure (London, England : 1993)
Oct 25, 2024
The high binding affinity of antibodies toward their cognate targets is key to eliciting effective immune responses, as well as to the use of antibodies as research and therapeutic tools. Here, we propose ANTIPASTI, a convolutional neural network mod...
Pretrainable geometric graph neural network for antibody affinity maturation.
Nature communications
Sep 6, 2024
Increasing the binding affinity of an antibody to its target antigen is a crucial task in antibody therapeutics development. This paper presents a pretrainable geometric graph neural network, GearBind, and explores its potential in in silico affinity...
Leveraging artificial intelligence in vaccine development: A narrative review.
Journal of microbiological methods
Jul 15, 2024
Vaccine development stands as a cornerstone of public health efforts, pivotal in curbing infectious diseases and reducing global morbidity and mortality. However, traditional vaccine development methods are often time-consuming, costly, and inefficie...
Machine-learning-based structural analysis of interactions between antibodies and antigens.
Bio Systems
Jul 2, 2024
Computational analysis of paratope-epitope interactions between antibodies and their corresponding antigens can facilitate our understanding of the molecular mechanism underlying humoral immunity and boost the design of new therapeutics for many dise...
Prediction of Paratope-Epitope Pairs Using Convolutional Neural Networks.
International journal of molecular sciences
May 16, 2024
Antibodies play a central role in the adaptive immune response of vertebrates through the specific recognition of exogenous or endogenous antigens. The rational design of antibodies has a wide range of biotechnological and medical applications, such ...
Accurate structure prediction of biomolecular interactions with AlphaFold 3.
Nature
May 8, 2024
The introduction of AlphaFold 2 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design. Here we describe our AlphaFold 3 model with a substantially...
Beyond Natural Immune Repertoires: Synthetic Antibodies.
Cold Spring Harbor protocols
Apr 1, 2024
Synthetic antibody libraries, in which the antigen-binding sites are precisely designed, offer unparalleled precision in antibody engineering, exceeding the potential of natural immune repertoires and constituting a novel generation of research tools...
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