Molecular Modeling

Molecular Modeling

Unparalleled insight into your antibody discovery

Predicting which antibodies will or will not bind to a specific target is a skill that doesn’t come easy. Although antibodies have the power to bind targets with high affinity and high specificity, understanding the precise atomic interactions that define the “lock-and-key” relationship between an antibody and antigen makes predictive modeling a very tall order.

Molecular modeling methods have advanced to a point where a realistic view of intra- and inter- molecular interactions at a resolution that isn’t available through conventional lab instruments is possible. Recent advances in molecular 3D modeling have been successful in predicting the folding of proteins and atomic interactions within a protein, and even between two proteins, using amino acid sequences alone.

Antigen Modeling Figure copy.001-2

Modeling representations of D614 and G614 SARS-CoV-2 protein from S591 through N710. A. I-TASSER -derived models using SARS-CoV spike protein PDB ID: 5X58 as the template. The furin cleavage domain 682-RRARS-686 is shown in orange, and D614 (left) or G614 (right) are shown in magenta. Residues between 614 and the cleavage domain are shown in green.


By leveraging our molecular modeling capabilities and expertise, together we can explore what shape—quite literally—your research should take. The structure of your target antigen can come into sharper focus through in silico modeling of antigen structure and even specific antigen-antibody interactions. 

Those fresh insights have both bottom-line clinical and financial value: Adding molecular 3D modeling to the mix reduces the time and cost of antibody discovery. Modeling can answer questions quickly, identify promising strategies, and save time and effort at the bench. 

With a suite of advanced structural modeling services, Antibody Solutions can provide insights into antibody discovery for your project through:

  • Antigen Modeling — Assess the structure of target domains
  • Antigen Design — Guide surrogate antigen synthesis, examples include
    • Peptides mimicking native protein domains
  • Antibody Modeling — Identify CDR shape and solvent exposed residues 
  • Antibody/Antigen Docking — Identify critical antigen and antibody contact surfaces and residues
  • Antibody/Antigen Epitope Analysis — Identify fine specificity of competitive antibodies 
  • Antibody Engineering — Improve affinity and cross-species antigen binding
  • Antibody Developability — Assess sequence liabilities

In keeping with our unwavering commitment to scientific rigor, modeling can be complemented by our build-and-test services such as antigen expression, analytical assays, protein chemistry, and recombinant antibody expression. 

Since amino acids fold, curl and twirl every which way, it’s helpful to put technology to work that can help uncoil a straighter line to successful antibody engagement. So the next time you’d like to get a clearer vision of the most efficient path forward for your research, just connect with us and we can explore our molecular modeling platform together. 

You can learn more about the advantages of molecular modeling by downloading this poster, “Generation Using a Molecular Modeling Platform to Guide Therapeutic Antibody Discovery.”