6 papers
MolChord: Structure-Sequence Alignment for Protein-Guided Drug Design
Wei Zhang, Zekun Guo, Yingce Xia +4
Structure-based drug design (SBDD), which maps target proteins to candidate molecular ligands, is a fundamental task in drug discovery. Effectively aligning protein structural repr…
An Analysis and Mitigation of the Reversal Curse
Ang Lv, Kaiyi Zhang, Shufang Xie +4
Recent research observed a noteworthy phenomenon in large language models (LLMs), referred to as the ``reversal curse.'' The reversal curse is that when dealing with two entities,…
SFM-Protein: Integrative Co-evolutionary Pre-training for Advanced Protein Sequence Representation
Liang He, Peiran Jin, Yaosen Min +7
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and…
Exploiting Pre-trained Models for Drug Target Affinity Prediction with Nearest Neighbors
Qizhi Pei, Lijun Wu, Zhenyu He +4
Drug-Target binding Affinity (DTA) prediction is essential for drug discovery. Despite the application of deep learning methods to DTA prediction, the achieved accuracy remain subo…
BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning
Qizhi Pei, Lijun Wu, Kaiyuan Gao +6
Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However,…
Retrosynthetic Planning with Dual Value Networks
Guoqing Liu, Di Xue, Shufang Xie +7
Retrosynthesis, which aims to find a route to synthesize a target molecule from commercially available starting materials, is a critical task in drug discovery and materials design…