Accelerate Antibody Design: ABodyBuilder3 is Now Available on Vecura

What is ABodyBuilder3?

ABodyBuilder3 is a specialized deep-learning model designed to predict the 3D atomic structure of paired antibody variable domains (VH/VL) directly from their amino-acid sequences. Unlike general-purpose protein structure predictors, this model is trained specifically on antibody data, enabling it to deliver high-accuracy structural models in under two seconds. By eliminating the need for Multiple Sequence Alignments (MSA) or template searches, it provides a self-contained, reproducible pipeline for researchers.

It helps users rapidly generate structural insights for antibody engineering, facilitating the evaluation of CDR loop conformations. It is especially useful for early-stage therapeutic development where obtaining reliable atomic models of hypervariable regions—particularly the CDRH3 loop—is a common bottleneck.

What can users do with ABodyBuilder3 on Vecura?

With ABodyBuilder3 on Vecura, users can:

• Predict the full 3D atomic structure of antibody Fv fragments from input sequences.
• Retrieve PDB-formatted files for immediate integration into docking or molecular visualization workflows.
• Assess the reliability of predictions using per-residue pLDDT confidence scores.
• Evaluate the overall structural confidence through a mean pLDDT summary metric.

What the output means

The output provides a 3D atomic model in PDB format, alongside per-residue pLDDT confidence scores. These scores, ranging from 0 to 100, indicate the local model accuracy; values above 90 represent high confidence, while lower scores signal potentially flexible regions.

This output should be used to support scientific decision making. It does not replace experimental validation.

Why this matters

Obtaining high-quality structural models of antibodies is crucial for predicting binding interactions and engineering desired pharmacological properties. The hypervariability of the CDRH3 loop has historically made in silico modeling challenging. ABodyBuilder3 addresses this by leveraging a state-of-the-art structure module that achieves superior accuracy on these critical regions.

By offering this capability directly within the Vecura platform, researchers can bypass the technical overhead of local installation and database management, significantly accelerating the design-build-test cycle in antibody discovery.

• Developed by: Exscientia
• Source: Official GitHub Repository
• Reference: Kenlay et al., Bioinformatics 40(10), 2024