ANTIBODY MODELING

Generate highly accurate 3D models of antibodies and antibody fragments in minutes.

Use NovaFold Antibody to predict highly accurate 3D antibody models from sequence data in minutes.

Antibody modeling is an important tool for antibody design and optimization, where prediction accuracy is critical. Within Protean 3D, the NovaFold Antibody method combines homology modeling for framework regions with fragment-based or ab initio modeling for hypervariable loop regions to generate highly accurate antibody structure predictions.

Protean 3D features an intuitive prediction wizard designed to simplify antibody-antigen modeling workflows. Guided setup tools walk users through sequence entry, prediction configuration, and modeling parameter selection, making advanced AI-based antibody modeling easier to manage and reproduce.

Simply provide sequences for the light chain, heavy chain, or both to generate annotated antibody models, including predicted structures, likely template matches, and complementary determining region (CDR) loop annotations. Resulting models can be visualized, analyzed, and customized within Protean 3D for downstream analysis and publication-quality rendering. Antibody models can also be used in conjunction with protein docking workflows to predict antibody-antigen interactions.

To support antibody screening and interaction studies, the wizard allows users to define a fixed antibody or antigen structure and evaluate it against multiple variable partner structures within the same workflow. This enables efficient analysis of candidate binding interactions across a range of antibodies or antigens.

Antibody modeling in 4 simple steps

Step 1

Provide sequences for the light chain, the heavy chain, or both

Step 2

Run antibody modeling prediction

Step 3

View and analyze predicted antibody models with annotations

Step 4

Customize rendering to prepare images for publication

Quality models and useful insights

“Using the suite of DNASTAR programs, NovaFold, NovaFold Antibody, and NovaDock, I have generated functional models of antibody-antigen complexes from the component’s amino acid sequences. The quality of the models and the useful insights they generate more than justify the effort and computing time.”

Dr. Kurt Deshayes, Antibody Solutions

FAQs

How do I access antibody modeling predictions?

Antibody structure predictions are available through NovaCloud using bundled prediction tokens included with Lasergene Protein or through NovaLocal for locally hosted prediction workflows and high-throughput modeling studies.

What file types are supported for the light chain and heavy chain sequences required for antibody modeling?

Protean 3D supports the following protein file formats: .aa, .fap, .fas, .fasta, .gp, .gbk, .sbd, .pro.

What is the prediction method used for antibody structure modeling by NovaFold Antibody?

The NovaFold Antibody algorithm utilizes a combination of homology modeling and ab initio loop prediction, resulting in highly accurate predictions. During modeling, NovaFold Antibody searches the input sequence(s) against thousands of non-redundant protein antibody structures from PDB and finds the best…

During modeling, NovaFold Antibody gives particular consideration to the complementary determining region (CDR) loops, hypervariable regions of an antibody that react dominantly with an antigen. The three CDR loops on the heavy chain are known as H1, H2 and H3, while the three on the light chain are L1, L2 and L3. H3 is commonly the most important region in antigen binding. Due to its increased length and flexibility, it is also the most difficult to model. As such, NovaFold Antibody limits H3 loop modeling to fifteen or fewer residues, a length commonly seen in antibody modeling problems. Finally, NovaFold Antibody performs energy minimization calculations to construct the final predicted structure model for the antibody chain or complex. This entire process takes approximately 5-15 minutes on a standard workstation computer.

How do I visualize the predicted antibody models?

After running an antibody modeling prediction using NovaFold Antibody, the resulting .antibody structure file can be viewed and analyzed in Protean 3D, part of Lasergene Protein. Protean 3D provides a graphical view of the structures, which allows you to visualize annotated features, including the six annotated CDR loops for light and heavy chains.

What details are available for each antibody model?

Available statistics for each antibody model include biophysical properties, structural properties, as well as details for each annotated hypervariable loop region. Results of the completed NovaFold Antibody prediction are also shown in a specialized report summarizing the identified loops and the template structures used for modeling.

Can I export an antibody structure model for publication?

Yes. Protean 3D lets you export the antibody structure itself or an image of the structure. To export the predicted antibody structure as a .pdb or .cif file, use File>Export Data > Export Structure. To export an image of the predicted antibody model in .png, .jpg or .gif format, use File > Export Image > Structure.

How can I model antibody-antigen interactions?

Antibody models generated using the NovaFold Antibody method can be used with NovaDock in Protean 3D to predict antibody-antigen interactions. Antibody structures can serve as ligands or receptors in docking predictions to model binding interactions and analyze predicted complexes. Simply provide ligand and receptor PDB or structure files and optionally define specific residue contacts between binding partners. The NovaDock method predicts the three-dimensional structure of the resulting macromolecular complex and provides metrics such as energy score, cluster size, and ligand contact information to support downstream analysis.

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