5 papers
BioMatrix: Towards a Comprehensive Biological Foundation Model Spanning the Modality Matrix of Sequences, Structures, and Language
Qizhi Pei, Zhimeng Zhou, Yi Duan +9
We present BioMatrix, the first multimodal foundation model that natively integrates sequences, structures, and natural language for both molecules and proteins within a single dec…
Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey
Qizhi Pei, Zhimeng Zhou, Kaiyuan Gao +6
The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and…
3D-MolT5: Leveraging Discrete Structural Information for Molecule-Text Modeling
Qizhi Pei, Rui Yan, Kaiyuan Gao +2
The integration of molecular and natural language representations has emerged as a focal point in molecular science, with recent advancements in Language Models (LMs) demonstrating…
FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation
Kaiyuan Gao, Qizhi Pei, Gongbo Zhang +3
Molecular docking is a pivotal process in drug discovery. While traditional techniques rely on extensive sampling and simulation governed by physical principles, these methods are…
Fast and Accurate Blind Flexible Docking
Zizhuo Zhang, Lijun Wu, Kaiyuan Gao +3
Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery. However, existing docking methods…