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EasyNano: rapid epitope-targeted nanobody CDR design via differentiable distogram optimization with ESMFold2
Yue Hu, Wanyu Cheng, Junqing Wang +1
Computational design of nanobodies that bind user-specified protein epitopes could transform therapeutic development, but current methods either rely on stochastic sampling requiri…
Interpretable enzyme function prediction via sparse autoencoder features of ESMC across the microbial protein universe
Yue Hu, Wanyu Cheng, Junqing Wang +1
Microbial genomes and metagenomes contain millions of proteins whose enzymatic functions remain unknown, the enzyme dark matter. While deep learning has improved protein function p…
TurboESM: Ultra-Efficient 3-Bit KV Cache Quantization for Protein Language Models with Orthogonal Rotation and QJL Correction
Yue Hu, Junqing Wang, Yingchao Liu
The rapid scaling of Protein Language Models (PLMs) has unlocked unprecedented accuracy in protein structure prediction and design, but the quadratic memory growth of the Key-Value…
AntibodyDesignBFN: High-Fidelity Fixed-Backbone Antibody Design via Discrete Bayesian Flow Networks
Yue Hu, Feng Tao, Junqing Wang +1
The computational design of antibodies with high specificity and affinity is a cornerstone of modern therapeutic development. While deep generative models have demonstrated potenti…