Protap: General Protein Pretraining or Domain-Specific Designs? Benchmarking Protein Modeling on Realistic Applications
Published in arXiv, 2025
We introduce Protap, a comprehensive benchmark that systematically compares backbone architectures, pretraining strategies, and domain-specific models across diverse and realistic downstream protein applications. Protap covers five applications including enzyme-catalyzed protein cleavage site prediction and targeted protein degradation.
Recommended citation: Shuo Yan, Yuliang Yan, Bin Ma, Chenao Li, Haochun Tang, Jiahua Lu, Minhua Lin, Yuyuan Feng, Enyan Dai. (2025). "Protap: Benchmarking Protein Modeling on Realistic Applications." arXiv:2506.02052.