AIMC Topic: Binding Sites, Antibody

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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...
Antibody Affinity Binding Sites, Antibody Antibodies Antigens Antigen-Antibody Complex Humans Neural Networks, Computer Deep Learning Protein Binding Models, Molecular
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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...
Deep Learning Protein Binding Computational Biology Humans Machine Learning Binding Sites, Antibody Antigens Binding Sites Antigen-Antibody Complex Antibodies Epitopes
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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 ...
Epitopes Antigens Antigen-Antibody Complex Molecular Docking Simulation Antibodies Binding Sites, Antibody Humans Neural Networks, Computer Machine Learning
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Leveraging Sequential and Spatial Neighbors Information by Using CNNs Linked With GCNs for Paratope Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Feb 3, 2022
Antibodies consisting of variable and constant regions, are a special type of proteins playing a vital role in immune system of the vertebrate. They have the remarkable ability to bind a large range of diverse antigens with extraordinary affinity and...
Binding Sites, Antibody Proteins Antibodies Neural Networks, Computer Algorithms
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Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification.

PLoS computational biology Mar 29, 2021
High-throughput B-cell sequencing has opened up new avenues for investigating complex mechanisms underlying our adaptive immune response. These technological advances drive data generation and the need to mine and analyze the information contained in...
Neural Networks, Computer Deep Learning Image Processing, Computer-Assisted Antibodies, Viral Computational Biology Models, Molecular Humans Virus Diseases Binding Sites, Antibody Antibodies Epitopes
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Prediction of Contact Residues in Anti-HIV Neutralizing Antibody by Deep Learning.

Japanese journal of infectious diseases Jan 31, 2020
The monoclonal antibody 1C10 targets the V3 loop of HIV-1 and neutralizes a broad range of clade B viruses. However, the mode of interaction between 1C10 and the V3 loop remains unclear because crystallization of 1C10 and the V3 peptide was unsuccess...
HIV Envelope Protein gp120 Binding Sites, Antibody Amino Acid Substitution HIV Antibodies Peptide Fragments Humans Antibodies, Neutralizing Molecular Docking Simulation Amino Acid Sequence Deep Learning Antibodies, Monoclonal
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Accurate Prediction for Antibody Resistance of Clinical HIV-1 Isolates.

Scientific reports Oct 11, 2019
Broadly neutralizing antibodies (bNAbs) targeting the HIV-1 envelope glycoprotein (Env) have promising utility in prevention and treatment of HIV-1 infection, and several are currently undergoing clinical trials. Due to the high sequence diversity an...
Neutralization Tests env Gene Products, Human Immunodeficiency Virus Broadly Neutralizing Antibodies Immunoglobulin Idiotypes Prognosis HIV-1 HIV Antibodies Humans Deep Learning Data Accuracy Epitope Mapping Computer Simulation HIV Infections Drug Resistance, Viral Binding Sites, Antibody
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ParaSurf: a surface-based deep learning approach for paratope-antigen interaction prediction.

Bioinformatics (Oxford, England) Feb 4, 2025
MOTIVATION: Identifying antibody binding sites, is crucial for developing vaccines and therapeutic antibodies, processes that are time-consuming and costly. Accurate prediction of the paratope's binding site can speed up the development by improving ...
Software Models, Molecular Antigens Binding Sites, Antibody Deep Learning Protein Binding Computational Biology
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Paragraph-antibody paratope prediction using graph neural networks with minimal feature vectors.

Bioinformatics (Oxford, England) Jan 1, 2023
SUMMARY: The development of new vaccines and antibody therapeutics typically takes several years and requires over $1bn in investment. Accurate knowledge of the paratope (antibody binding site) can speed up and reduce the cost of this process by impr...
Antibodies Antigens Binding Sites, Antibody Neural Networks, Computer Software
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In silico proof of principle of machine learning-based antibody design at unconstrained scale.

mAbs Jan 1, 2022
Generative machine learning (ML) has been postulated to become a major driver in the computational design of antigen-specific monoclonal antibodies (mAb). However, efforts to confirm this hypothesis have been hindered by the infeasibility of testing ...
Antibodies, Monoclonal Epitopes Binding Sites, Antibody Antigen-Antibody Reactions Machine Learning
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