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Homology Antibody Modeling

Homology antibody modeling is one of the most commonly used antibody modeling methods. Taking advantage of our unchallenged experience in antibody modeling, Creative Biolabs is committed to providing customer expected antibody homology models with high accuracy for your research purpose.

Computational structure prediction of antibodies is an essential step in the modeling and creating new antibodies with desired therapeutic properties. As the variable domains (Fvs) of the heavy and light chain responsible to most or all of the specificity of an antibody for its antigen target, they are of special interest. The Fv contains two regions: the hypervariable regions also called complementarity-determining regions (CDRs), and the framework regions (FRs). The CDRs consisted of 6 hypervariable loops on the surface of the antibody, including H1, H2 and H3 of the heavy variable domain (VL), and L1, L2 and L3 of the light variable domain (VH). On account of the extremely conserved nature of the FRs of the VL and VH domains, study into Fv structure prediction has mainly focused on the prediction of the 6 CDR loops.

Homology Antibody ModelingFig 1. Schematic diagram of the homology model of cAb VHH CAB-RN05 (1BZQ). Part A shows the Ag-eye view of the paratope showing the CDR diversity in the 10 lowest energy homology models. Part B shows the Side view of the LowRMS homology model superimposed on the native framework. (Sircar, A., 2011)

Homology Modeling

Generally, homologous antibodies with related amino acid sequences have similar 3D structures. Homology modeling takes advantage of comparative approaches to produce models for a target antibody through one or more related antibody with known 3D structure. The coordinates of the model are formed on account of alignments between the target's and template's amino acid sequences, which define the correspondence between residues in both antibodies. However, the quality of a computational model decides its usefulness for specific biomedical applications. Thus, model quality estimation approaches are utilized to measure unreliable or erroneous regions in the resulting models, and to evaluate the overall accuracy of a model. Nowadays, homology modeling is the most accurate computational approach possible to commonly produce models of sufficient quality for a variety of applications in life science research.

Antibody Homology Model Process

Creative Biolabs has established a unique computational 3D structure prediction platform to generate an antibody homology model.

  • The first step in homology modeling is to discover a template with high sequence similarity to our unknown protein, which has a known structure.
  • Then, a sequence alignment is offered, and prior to aligning the two sequences, the template structure is cleaned. After these two steps, a template structure and a good sequence alignment are obtained.
  • The third step is to automatically construct a series of homology models and select the highest quality one.

After building of homology models, we offer several methods for homology models analysis. Besides, there is a crucial step in building an antibody homology model: identification and refinement of CDR Loops. Identification of the CDRs is able to be performed through visual analysis with graphical tools or via knowledge-based approaches. Refinement of the CDRs will be done on our PreciAb™ platform. Finally, additional analysis of a novel homology model should contain various calculations for estimating model quality.

Based on our well-established homology antibody modeling platform, Creative Biolabs can build high-quality antibody homology models for the antibodies. And our resulting models will contribute greatly to the humanization, maturation or other applications of your antibodies. We also offer other antibody structure modeling services. Please feel free to contact us for more information and a detailed quote.

References

  1. Sircar, A., (2011). “Analysis and modeling of the variable region of camelid single-domain antibodies.” The Journal of Immunology, 186(11), 6357-6367.
  2. Bujotzek, A., (2015,). “MoFvAb: Modeling the Fv region of antibodies.” Taylor & Francis, 7(5): 838-852.

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