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ANTIBODY MODELING

Generate highly accurate models of antibodies and antibody fragments in minutes. PRICING SCHEDULE A DEMO

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

Antibody modeling is an important tool for antibody design and optimization and accuracy is paramount. Many antibody modeling tools rely solely on homology modeling, but NovaFold Antibody’s unique algorithm generates models of antibodies and antibody fragments by combining homology modeling for framework regions and fragment-based or ab initio modeling for hypervariable loop regions, resulting in highly accurate antibody structure predictions. Simply provide sequences for the light chain, the heavy chain, or both, and NovaFold Antibody will return an annotated report that includes the predicted antibody models, as well as the highest likelihood heavy chain and light chain templates and annotations for locations of CDR loops. Easily view antibody modeling results with annotations in Protean 3D, part of Lasergene Protein, which allows you to fully customize the rendering to aid in visualization, or to prepare publication-quality images to export. Antibody modeling with NovaFold Antibody can also be used in conjunction with NovaDock to predict the structure and binding of antibody-antigen complexes.

Antibody modeling in 4 simple steps

Antibody Modeling Step 1

Step 1

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

Antibody Modeling Step 2

Step 2

Run antibody modeling prediction

Antibody Modeling Step 3

Step 3

View and analyze predicted antibody models with annotations

Antibody Modeling Step 4

Step 4

Customize rendering to prepare images for publication

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Learn more about Antibody Modeling

Resources | Tutorials | FAQs | User Guide

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Resources

Please see our resources below for more information on antibody modeling.

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High-Resolution in silico Protein Structure Prediction and Docking

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High Resolution Protein and Antibody Modeling with NovaFold and NovaFold Antibody

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How Can DNASTAR’s Protein Tools Help You?

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Why Structure Prediction Matters

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Nova Applications on Mac: Bringing the Power of Protein Modeling to the Desktop

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Tutorials

Watch one of our videos or check out our user guide to learn more about using NovaFold Antibody for antibody modeling.

Lasergene Protein Overview

This video gives an overview of Lasergene Protein, consisting of Protean 3D, plus the optional services NovaFold, NovaFold Antibody and NovaDock.

NovaDock for Protein-Protein Docking Analysis

This video demonstrates how to predict protein-protein binding interactions using NovaDock.

Coloring a Structure in Protean 3D According to Features or Properties

This video shows how to apply a surface to a molecular structure in Protean 3D, how to color a selected feature, and how to color the entire structure in accordance with a selected biophysical or immunogenetic property.

Protein Structure Alignment in Protean 3D

In this video, we show you how to align protein structures in Protean 3D in order to evaluate structural similarity.

FAQs

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 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…

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 template matches for the chain or complex.

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.

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How do I visualize the predicted antibody models?

After running an antibody modeling prediction in NovaFold Antibody, the resulting .antibody structure file can be viewed and analyzed in Protean 3D, part of Lasergene Protein.  Protean 3D provides…

After running an antibody modeling prediction in 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.

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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?

You can use NovaDock, part of Lasergene Protein, to predict the structure of antibody-antigen complexes by inputting the antibody and antigen structures. Simply provide your ligand and receptor PDB…

You can use NovaDock, part of Lasergene Protein, to predict the structure of antibody-antigen complexes by inputting the antibody and antigen structures. Simply provide your ligand and receptor PDB or structure files within NovaDock, proposing specific residue contacts between the binding partners if desired. NovaDock will then predict the three-dimensional structure of the macromolecular complex and provide energy score, cluster size, and number of ligand contacts for each model for analysis.

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