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mBER: A Breakthrough in Antibody Design
Scientists have developed mBER, a new open-source protein binder design system, which is achieving state-of-the-art success rates for de novo antibody design. While previous methods have shown promise for designing "minibinders," designing binders in specific formats like antibodies has been a significant challenge. mBER addresses this gap by successfully designing binders in the VHH antibody format, a major step forward for protein engineering.
How mBER Works
mBER is built on the ColabDesign framework and achieves its high success rates by including specific and informative sequence and structure conditioning information during the design process. The paper highlights that this approach allows for the design of format-specific binders without needing to retrain the underlying protein folding and language models. The tool was used to design over 1 million VHH binders against 436 diverse targets, with a significant binding success against 45% of the tested targets.
What is Tamarind Bio?
Tamarind Bio is a pioneering no-code bioinformatics platform built to democratize access to powerful computational tools for life scientists and researchers. Recognizing that many cutting-edge machine learning models are often difficult to deploy and use, Tamarind provides an intuitive, web-based environment that completely abstracts away the complexities of high-performance computing, software dependencies, and command-line interfaces.
The platform is designed provide easy access to biologists, chemists, and other researchers who may not have a background in programming or cloud infrastructure but want to run experimental models with their data. Key features include a user-friendly graphical interface for setting up and launching experiments, a robust API for integration into existing research pipelines, and an automated system for managing and scaling computational resources. By handling the technical heavy lifting, Tamarind empowers researchers to concentrate on their scientific questions and accelerate the pace of discovery.
Accelerating Discovery with mBER on Tamarind Bio
Using the mBER system on a platform like Tamarind Bio could accelerate antibody discovery and therapeutic development by providing a streamlined, high-throughput workflow.
Massive-Scale Screening: The mBER system was used to design and screen over 1 million binders, a scale that is computationally intensive and requires significant resources. By running mBER on Tamarind, researchers could leverage a scalable cloud infrastructure to perform such large-scale design and screening campaigns without needing to manage their own high-performance computing.
Rapid Design Cycles: The ability to design antibodies with state-of-the-art success rates in a single system would drastically shorten the discovery cycle for new therapeutics. Researchers could use mBER on the platform to quickly generate and prioritize promising antibody designs for experimental validation.
How to Use mBER on Tamarind Bio
To leverage mBER's power, researchers can:
Access the Platform: Begin by logging in to the tamarind.bio website.
Select mBER: From the list of available computational models, choose the mBER tool.
Input Target Information: Provide the protein target and, if desired, specific epitope information.
Run mBER Design: Select the mBER tool on the platform to initiate the de novo antibody design process.
Receive Final Designs: The platform will provide a list of computationally designed antibody-format binders, which can then be tested experimentally.