Antibody-antigen Complex Analysis

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Antibody-antigen Complex Analysis

Creative Biolabs possesses unchallenged experience in antibody-antigen complex analysis. Multiple services from Creative Biolabs are available for providing customers an antibody with desired properties and high affinity, including antibody-antigen complex modeling and paratope characterization.

Antibody-antigen Complexes

Antibodies serve as an increasingly important role in pharmaceutical development, as well as in basic research and industrial processes. However, there are some difficulties in designing and developing novel antibodies with desired properties, although antibodies having been characterized for several decades. For example, just given an antibody structure, we unable to predict whether it can bind a nucleic acid, protein or sugar, let alone the specific antigen or conformational epitope that it recognizes. Therefore, the study of antibody-antigen complex can give our knowledge of the common principles of recognition, as well as gives us the basis for the successful design of novel molecules or the rational optimization of existing ones. Generally, obtain the three-dimensional structure of antibody-antigen complexes is the best way to study atomic interaction. This strategy is achieved by experimental techniques such as X-ray crystallography, which is a long laborious process with high failure rate. Due to the progress in algorithms and processing power, now we are able to use computational techniques for the structural analysis of intermolecular complexes.

Antibody-antigen Complex AnalysisFig 1. Structure of the PfCyRPA/c12 complex. Part A exhibits that the major interface is made by interactions between the light chain of c12 and blade 2 of PfCyRPA. Part A exhibits the details of the interface viewed from top onto the CDR loops. (Favuzza, P.,2017)

Antibody-antigen Complex Modeling

Creative Biolabs has established an advanced antibody-antigen complex modeling process based on the computational docking. In a classical docking protocol, the structures of the antigen and antibody are separated by about 25 Å and then brought together by the chosen algorithm. To docking the antibody-antigen complexes, firstly, it is necessary to obtain the structures of the isolated antigen and antibody. After chosen or obtained the starting structures for antibody and antigen, the molecules are then brought together by the preferred algorithm. During the computational docking process, there remain two problems: finding the correct solution, which is often performed by changing the relative position of the partners and repeating the calculation thousands of times; discriminating the correct solution from the inaccurate ones via utilizing a so-called―scoring function.

Paratope Characterization

Paratope is a part of the antibody's Fv region and comprises parts of the antibody's heavy and light chains. Creative Biolabs has developed a comprehensive computational procedure to predict paratope residues and their partners. This novel procedure mainly contains three parts: molecular dynamics (MD) simulations, rigid-body docking, and homology modeling. With the computational procedure, it is available to determine key paratope residues on the target antibody and their epitope on the antigen.

With our high-quality antibody-antigen complex analysis service, the experienced scientists here at Creative Biolabs are dedicated to helping you develop novel antibodies. We also provide other various services regarding epitope-specific antibody design. Please feel free to contact us for more information and a detailed quote.


  1. Favuzza, P., (2017). “Structure of the malaria vaccine candidate antigen CyRPA and its complex with a parasite invasion inhibitory antibody.” eLife, 6.
  2. Pedotti, M., (2011). “Computational docking of antibody-antigen complexes, opportunities and pitfalls illustrated by influenza hemagglutinin.” International journal of molecular sciences, 12(1), 226-251.
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