Creative BioMart provides antibody-antigen docking service for structural characterization of antibody (Fv, Fab, or full antibody) and antigen complexes, which is of practical significance to pharmaceutical and biological research. With years of protein engineering research experience, we can provide you with the best quality and most professional services. If you are interested in our services, please do not hesitate to contact us for more information.

Antibodies are a key protein of the immune system. Antibodies bind tightly and specifically to antigens to block their activity or label them for destruction. Over 3000 antibody structures are stored in the Protein Data Bank (PDB) and are increasingly used as medicines. Nuclear magnetic resonance (NMR) and X-ray crystallography provide various levels of information about key antibody and antigen residues involved in interactions, but most of them require high cost and effort. Furthermore, the enormous size of the immune reserve and the number of antigenic targets. Over the years, different docking algorithms have been developed to predict and characterize the three-dimensional (3D) structure of antibody-antigen complexes, playing an increasingly important role in drug development, basic research, and industrial processes.

Fig 1. Flow of computational antibody design. (Kuroda D, et al., 2012)

Accurate predictive modeling of antibody-antigen complex structures and structure-based antibody design remain major challenges in biology, with implications for biotherapeutics, immunization, and vaccines. Creative BioMart utilizes various antigen-antibody docking computational softwares to accurately predict the structure of antibody-antigen complexes. Implementations use prior knowledge (e.g., hypervariable loops) in the modeling process in various ways, ordering the models sequentially according to a specific scoring function to identify or predict models that are close to the true conformation.

We use advanced computational docking techniques to predict the 3D structure of the antibody from the sequence, taking into account the flexible and/or uncertain regions of the antibody in the CDR regions (especially the H3 loop), and then perform robust antibody-antigen docking. The process is as follows:

(1) Annotation sequence.

(2) Modeling framework.

(3) Modeling CDR loops and optimizing VH-VL orientation.

(4) Predicted paratope.

(5) Epitopes and antibody-antigen contact residues.

Features of Antibody-Antigen Docking

• A software suite that allows testing of assembly flexibility in assemblies to improve H3 loop conformation.
• Antibody-antigen docking was successfully achieved starting only from the antigen structure and antibody sequence.
• Using multiple models to represent conformational ensembles of antibodies, antigens, or both.
• It can be run fully automatically through a computing server or manually on a computer where the user controls the individual steps.
• Dedicated scoring function for evaluating antigen-antibody interactions.
• Useful for new therapeutic antibodies whose coordinates cannot be determined experimentally, docking models can help identify epitopes.

References

1. Ambrosetti F, Jiménez-García B, Roel-Touris J, et al.. (2020) Modeling antibody-antigen complexes by information-driven docking[J]. Structure. 28(1): 119-129. e2.
2. Guest J D, Vreven T, Zhou J, et al.. (2021) An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants[J]. Structure. 29(6): 606-621. e5.
3. Kuroda D, Shirai H, Jacobson M P, et al. (2012) Computer-aided antibody design[J]. Protein engineering, design & selection. 25(10): 507-522.

• Protein-Carbohydrate Docking
• Protein-Ligand Docking
• Protein-Lipid Docking
• Protein-Nucleic Acid Docking
• Protein-Peptide Docking
• Protein-Protein Docking