mBER Open Now Available on Vecura

What is mBER Open?

mBER Open is an open-source protein design framework that generates novel VHH (nanobody) antibody sequences capable of binding a user-supplied target protein structure. The model uses a three-stage process to refine binder sequences and predict 3D complex structures, significantly reducing the time from design to candidate. It is especially useful for researchers in biotechnology and pharmaceuticals who need to design specific binders for their targets.

What can users do with mBER Open on Vecura?

With mBER Open on Vecura, users can:

• Design de novo VHH nanobody sequences that are predicted to bind a target protein

• Optimize the CDR loop sequences for high-affinity binding

• Generate a 3D structural hypothesis for further engineering or affinity maturation

• Bypass the need for large library screening and immunization campaigns

• Obtain directly testable binder sequences with predicted 3D complex structures

What the output means

The output provides designed VHH amino acid sequences, interface and global predicted TM-scores, per-residue structural confidence, and file paths to the relaxed complex and monomer PDB structures. These outputs should be used to support scientific decision making, such as selecting candidates for synthesis and experimental validation. It does not replace the need for biophysical validation.

Why this matters

Antibody engineering has traditionally required extensive and time-consuming experimental screening. mBER Open offers a computational approach to accelerate the discovery of high-affinity binders, enabling scientists to focus on downstream applications such as therapeutic development, diagnostics, and research. By leveraging state-of-the-art deep learning models like AlphaFold-Multimer, mBER Open can produce structurally confident designs that are ready for testing in the lab.

• Developed by: Manifold Bio

• Source: Original paper (bioRxiv), Official GitHub repo

• Reference: Introducing mBER - Manifold Bio announcement