1 citations · 1 across the 3 of their papers we have counts for
7 papers
CONFIDE: Hallucination Assessment for Reliable Biomolecular Structure Prediction and Design
Zijun Gao, Mutian He, Shijia Sun +8
Reliable evaluation of protein structure predictions remains challenging, as metrics like pLDDT capture energetic stability but often miss subtle errors such as atomic clashes or c…
Lost in Tokenization: Context as the Key to Unlocking Biomolecular Understanding in Scientific LLMs
Kai Zhuang, Jiawei Zhang, Yumou Liu +10
Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when proc…
Learning the PTM Code through a Coarse-to-Fine, Mechanism-Aware Framework
Jingjie Zhang, Hanqun Cao, Zijun Gao +8
Post-translational modifications (PTMs) form a combinatorial "code" that regulates protein function, yet deciphering this code - linking modified sites to their catalytic enzymes -…
A deep reinforcement learning platform for antibiotic discovery
Hanqun Cao, Marcelo D. T. Torres, Jingjie Zhang +8
Antimicrobial resistance (AMR) is projected to cause up to 10 million deaths annually by 2050, underscoring the urgent need for new antibiotics. Here we present ApexAmphion, a deep…
Lightweight MSA Design Advances Protein Folding From Evolutionary Embeddings
Hanqun Cao, Xinyi Zhou, Zijun Gao +7
Protein structure prediction often hinges on multiple sequence alignments (MSAs), which underperform on low-homology and orphan proteins. We introduce PLAME, a lightweight MSA desi…
SAGEPhos: Sage Bio-Coupled and Augmented Fusion for Phosphorylation Site Detection
Jingjie Zhang, Hanqun Cao, Zijun Gao +2
Phosphorylation site prediction based on kinase-substrate interaction plays a vital role in understanding cellular signaling pathways and disease mechanisms. Computational methods…