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Antibody Structure Modeling

Based on advanced in silico technologies, Creative Biolabs offers customized antibody structure modeling services. We take advantage of computational modeling approaches to help customers predict the three-dimensional structure of antibodies. Based on ample experiences, we are confident in providing high-quality antibody structure modeling services to contribute greatly to your antibody development.

Antibody Modeling Strategy

Recently, antibodies are cumulatively used as diagnostic tools and therapeutic drugs, and an essential component of the antibody engineering process is the availability of high-quality three-dimensional structures. Although there are experimental approaches which enable to obtain structural models in atomic detail, such as NMR, X-ray crystallography, not all antibody structures can be generated through these methods. Besides, limited resources make it impossible to measure the structures of all of the sequences identified in high-throughput sequencing experiments. Thus, in order to bridge the sequence–structure gap, computational prediction approaches are employed. Importantly, these approaches are potent in diagnostics and drug discovery to define epitopes and help infer biological or therapeutic mechanisms. In general, there are two approaches used in antibody modeling: homology modeling and antibody initio (or de novo) modeling.

Antibody Structure ModelingFig.1 Ribbon views of three antibody structures: CR2-Ig, Crry-Ig and SC of IgA. These structures were determined by constrained scattering modelling. (Perkins, S. J., 2008)

Homology Modeling

Homology modeling takes advantages of the 3-D structures of protein molecules with similar sequences as ‘‘templates’’ and generate a structure depended on the template structures combined with the AA differences between the template and the modeled sequence. Usually, sequence databases and sequence alignment tools are required in homology modeling to screen the sequences to be used as templates, and structure databases are utilized to offer the coordinates of structures with closely related sequences. Moreover, minor refinements (e.g., those for side chains) are also used to improve the prediction accuracy. Homology modeling behaves great in accurately predicting the structure of the framework of the Fv region, because the overall fold of antibodies is extremely conserved.

Antibody de novo Modeling

Due to the low sequence similarity in the complementarity-determining regions (CDRs) and a corresponding structural divergence in the template, homology modeling is less successful to CDRs. Hence, the modeling of CDR loops is much more challenging. Usually, two main loop-modeling methods are used: loop grafting and de novo modeling. Essentially, loop grafting is a method that directly copies the crystal structure coordinates of a known loop of similar length. This approach performs quite well for CDR L1, L2, L3, H1 and H2 loops, but is less accurate in predicting the non-canonical structure of the H3 loop. By contrast, de novo modeling does not depend on existing structural templates for the loop regions. It enables to be utilized to predict, without bias, the conformation of these crucial antibody features.

Antibody Structure Modeling Services

Creative biolabs offers a variety of antibody structure modeling services for customers:

With our comprehensive modeling services, designing and engineering novel antibodies with desired therapeutic properties is available. We customize the service according to the specific requirements from the customers. We also provide other epitope-specific antibody design services. Please contact us for more information and a detailed quote.


  1. Perkins, S. J., (2008). “Structure determinations of human and chimaeric antibodies by solution scattering and constrained molecular modelling.”
  2. Zhao, Z., (2012). “Crystal structure and computational modeling of the fab fragment from a protective anti-ricin monoclonal antibody.” PloS one, 7(12), e52613.
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