VenusFactory: An Integrated System for Protein Engineering with Data Retrieval and Language Model Fine-Tuning

Natural language processing (NLP) has significantly influenced scientific domains beyond human language, including protein engineering, where pre-trained protein language models (PLMs) have demonstrated remarkable success. However, interdisciplinary adoption remains limited due to challenges in data collection, task benchmarking, and application. This work presents VENUSFACTORY, a versatile engine that integrates biological data retrieval, standardized task benchmarking, and modular finetuning of PLMs. VENUSFACTORY supports both computer science and biology communities with choices of both a command-line execution and a Gradio-based no-code interface, integrating 40+ protein-related datasets and 40+ popular PLMs. All implementations are open-sourced on https://github.com/a i4protein/VenusFactory .