Antibody-Antigen Interaction Modeling Service

Antibody-antigen interaction modeling involves the use of computational simulations to predict and analyze how antibodies recognize and bind to specific antigens, allowing understanding immune responses, design vaccines, and develop therapeutic antibodies. CD ComputaBio uses mainstream computational tools and algorithms to launch a one-stop antibody-antigen interaction modeling service, from structural modeling, molecular docking, molecular dynamics simulation to data analysis. We have extensive experience in computational biology and high-performance computing resources to accelerate the simulation process, save your time and ensure the accuracy of the results.

Introduction to Antibody-Antigen Interaction Modeling

Antibody-antigen interactions are fundamental to the immune response and play a critical role in recognizing and neutralizing pathogens such as viruses and bacteria. Detailed modeling of these interactions using advanced computational biology methods can provide insights into immune system function, aid vaccine design, and support the development of therapeutic antibodies. characteristics of typical antigen-antibody interactions include:

Binding Specificity - Antibodies have unique binding sites (paratopes) that specifically recognize and bind to specific regions (epitopes) on antigens. This specificity stems from the amino acid sequence and structural diversity of the antibody variable region, which enables them to discern many different antigens.
Non-Covalent Interactions - The binding between antibodies and antigens is mainly achieved through non-covalent interactions, involving forces such as hydrogen bonds, electrostatic interactions, van der Waals forces, and hydrophobic effects.
Affinity - Affinity is used to determine the strength of epitope binding to the antibody and to quantify the overall stability of the antibody-antigen complex. High-affinity binding enables antibodies to effectively neutralize or eliminate antigens.

Fig. 1 Antigen-antibody interaction analysis. (Kalim M, et al.; 2022)

Our Services

Thanks to its high-performance computational analysis platform and experienced team of experts, CD ComputaBio provides comprehensive antibody-antigen interaction modeling services to help customers gain a deeper understanding of the interaction mechanism between antibodies and antigens. Our antibody-antigen interaction modeling services cover a variety of molecular types and provide comprehensive modeling and molecular dynamics simulation analysis for different antigens and antibody structures, including but not limited to:

Antibody-Protein Interaction Modeling Service

Protein three-dimensional structure modeling and prediction.
Antigen epitope, including linear epitope and conformational epitope, identification and analysis.
Docking simulation of antibody variable region and protein antigen.
Interaction interface analysis and energy calculation.

Antibody-Peptide Interaction Modeling Service

Peptide structure modeling and conformation analysis.
Prediction of peptide-antibody binding mode.
Optimization of peptide design to improve immunogenicity or affinity.

Antibody-Polysaccharide Interaction Modeling Service

Modeling of polysaccharide structure, including complex sugar chains and branched structures.
Simulation of interaction between polysaccharide and antibody.
Identification of key glycosyl residues and their effects on immune response.

Antibody-Nucleic Acid Interaction Modeling Service

Prediction of nucleic acid secondary and tertiary structures.
Analysis of nucleic acid-antibody binding sites.
Study of interaction patterns to understand the mechanism of autoimmune response.

Antibody-Hapten Interaction Modeling Service

Modeling and property analysis of small molecules.
Construction of small molecule-carrier protein complexes.
Prediction of binding mode and affinity of small molecules and antibodies.

And More

Multi-component modeling of antibody-antigen complex.
Comprehensive analysis of your antigen of interest epitopes.
Customize computational strategies to accurately model and simulate complex antibody-antigen systems based on your specific research needs.

Workflow for Antibody-Antigen Interaction Modeling

Data Preparation and Modeling

Obtaining the crystal structure or NMR structure of the antibody and antigen from a protein database, such as PDB. If the structure is unknown, collect the amino acid sequences of the antibody and antigen. Use modeling software to perform homology modeling on the antibody and antigen, respectively.

Antibody-Antigen Docking

Using advanced computational biology tools to identify active sites, determine the location and conformation of complementary determining regions (CDRs), and potential antigen epitopes or known binding sites. On this basis, use professional docking software, such as RosettaDock, ZDOCK, and HADDOCK, to perform docking simulations on the pre-treated antibodies and antigens to generate a series of possible antibody-antigen complex conformations and screen out the best model.

Molecular Dynamics Simulations and Stability Assessment

Using molecular dynamics simulation software to assess the stability of the antibody-antigen complex and study the dynamic characteristics of the interaction.

Simulation Result Analysis

Using MM/PBSA or MM/GBSA methods to calculate the binding free energy, and perform residue decomposition of the binding energy to identify the amino acid residues that contribute most to the binding. In-depth analysis of antibody-antigen interactions, including hydrogen bond analysis, hydrophobic interactions, and salt bridge and π-π interactions.

Antibody Optimization Recommendations (Optional)

Based on the above analysis results, optimize the antibody to improve affinity specificity. Perform site-directed mutagenesis on amino acids that contribute significantly to binding to enhance antibody-antigen interactions.

CD ComputaBio relies on world-class technical expertise to provide customers with the best one-stop antibody-antigen interaction modeling services. Our goal is to help researchers and pharmaceutical companies deeply understand the interaction mechanism between antibodies and antigens, and accelerate the development of vaccines, diagnostic tools and therapeutic antibodies. Please feel free to contact us for more detailed information, our scientists will tailor the most reasonable plan for your project.

References:

Kalim M, et al. Bioengineering and computational analysis of programmed cell death ligand-1 monoclonal antibody. Front Immunol. 2022;13:1012499.
Ambrosetti F, et al. Modeling Antibody-Antigen Complexes by Information-Driven Docking. Structure. 2020;28(1):119-129.e2.
Gaudreault F, et al. Enhanced antibody-antigen structure prediction from molecular docking using AlphaFold2. Sci Rep. 2023;13(1):15107.

* For Research Use Only.

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