What is YueL?
YueL is a deep learning platform for predicting compound-protein interactions and binding affinity.
It scores a small molecule against a protein target, estimates the binding strength (pKd / Kd), and identifies key interaction hotspots at both atom and residue level. The model supports three protein input modes: amino acid sequence for sequence-based prediction, 3D structure (PDB or uploaded file) with automatic pocket discovery, and pre-prepared binding pocket files.
How to cite YueL
If you use YueL in a publication, please cite:
Wang, Jian, and Nikolay V. Dokholyan. "Yuel: improving the generalizability of structure-free compound–protein interaction prediction." Journal of Chemical Information and Modeling 62, no. 3 (2022): 463-471.
Wang, Jian, and Nikolay V. Dokholyan. "Leveraging Transfer Learning for Predicting Protein–Small-Molecule Interaction Predictions." Journal of Chemical Information and Modeling 65, no. 7 (2025): 3262-3269.