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Supported Applications

Germinal

  • Description

    is a pipeline for designing de novo antibodies against specified epitopes on target proteins. The pipeline follows a 3-step process: hallucination based on ColabDesign, selective sequence redesign with AbMPNN, and cofolding with a structure prediction model. Germinal is capable of designing both nanobodies and scFvs against user-specified residues on target proteins.

  • Usage

    To list all executables provided by Germinal, run: $ sbgrid-list germinal Copy to clipboard

  • Usage Notes

    Paths to model params need to be set in the config file. See documentation For convenience, an alias run_germinal.py is provided (instead of python run_germinal.py)

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install germinal Copy to clipboard Available operating systems: Linux 64

  • Primary Citation*

    L. S. Mille-Fragoso, J. N. Wang, C. L. Driscoll, H. Dai, T. Widatalla, X. Zhang, B. L. Hie, and X. J. Gao. 2025. Efficient generation of epitope-targeted de novo antibodies with Germinal. bioRxiv. Cold Spring Harbor Laboratory.


    • *Full citation information available through

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