OpenGerminal: an open-source implementation of the Germinal antibody design pipeline

Abstract

Germinal is a recently described computational pipeline for de novo antibody design that combines AlphaFold-Multimer hallucination with antibody language model guidance to generate epitope- targeted antibodies. Germinal identified binders with nanomolar-to-low-micromolar affinities by testing only 43-101 designs per target across four diverse antigens, establishing it as a practical tool for epitope-directed antibody design accessible to standard academic laboratories. As this architecture is itself very recent, systematic replacement and benchmarking of its individual components remains largely unexplored, yet offers a valuable opportunity to probe the robustness of the underlying design. We present OpenGerminal, which replaces PyRosetta with a fully open- source stack comprising OpenMM 8.5.1, FreeSASA, FASPR, Biopython, and sc-rs v1.0.0, and adopts AbLang1 (ablang2 v0.2.1) as the sole antibody language model in place of IgLM. Benchmarking on two VHH targets (PD-L1 and IL-3) reveals that OpenGerminal achieves a markedly higher cofolding pass rate (PD-L1: 33.7% vs. 18.6%; IL-3: 24.6% vs. 8.0%) with equivalent or improved Chai-1 structural confidence metrics in accepted designs, at the cost of a modest increase in per-trajectory computation time ([≥]1.5x). Multi-chain target support is also extended and verified to run without error on the official insulin example. OpenGerminal provides the first systematic benchmarking of IgLM versus AbLang1 within the Germinal architecture, and its fully open-source component stack broadens the range of deployment contexts in which the pipeline can be used. Availability and ImplementationSource code is freely available at https://github.com/teaninja/OpenGerminal under the Apache 2.0 license. Persistent archives with DOIs are available at https://doi.org/10.5281/zenodo.20755400 (code) and https://doi.org/10.5281/zenodo.20756013 (container image). OpenGerminal is implemented in Python and distributed as an Apptainer container (opengerminal_v1.0.0.sif). Installation instructions and example configurations are provided in the repository. Contactbh7bu@virginia.edu Supplementary informationSupplemental Figure 1 is available online.