Ding Luo's Homepage

Ding Luo 罗钉

luoding AT stu DOT xmu DOT edu DOT cn
Google Scholar, Github

I am a forth-year Ph.D. candidate at the Xiamen University College of Chemistry and Chemical Engineering, advised by Prof. Binju Wang.

RESEARCH

My current research focuses on leveraging AI and computational approaches to address specific challenges in chemistry and biology that are difficult to resolve through conventional experimental methods. Key applications include:

Applying deep learning to enzyme design, engineering, and discovery [Biorxiv'25, BDR'2024, Angew'2025];
Developing deep learning models to characterize protein-ligand interactions [JCIM'25, JCTC'24, JCTC'25]

In addition, I also have a general interest in:

Molecular simulations [J. Mol. Struct'22, Polycycl. Aromat. Comp'21, SAR QSAR Environ. Res'21, J. Mol. Liq.'21];

SELECTED PUBLICATIONS

AI for Science / Molecular simulations / Other Topics / All Publications (Google Scholar)

AI for Science

Catalytic pocket-informed augmentation of enzyme kinetic parameters prediction via hierarchical graph learning
Ding Luo, Xiaoyang Qu, Binju Wang^*. [PDF] [BiorXiv] [Code]
A Multimodal Ensemble Framework for Optimal Mutant Prediction and Computational Enzyme Engineering
Ding Luo^#, Huining Ji^#, Baodong Hu^#, Jinxing Cai^#, Kaiqi Wen, Xiaoyang Qu, Mingfeng Cao, Xinrui Zhao^*, Binju Wang^*.
Angew. Chem. Int. Ed. 2025, e21396.
[PDF] [Code]
Ligand-Conditioned Side Chain Packing for Flexible Molecular Docking
Ding Luo, Xiaoyang Qu, Dexin Lu, Yiqiu Wang, Lina Dong, Binju Wang^*.
J. Chem. Theory Comput. 2025, 21, 3, 1494–1505.
[PDF] [BiorXiv] [Code]
Enhancing Generalizability in Protein–Ligand Binding Affinity Prediction with Multimodal Contrastive Learning
Ding Luo, Dandan Liu, Xiaoyang Qu, Lina Dong, Binju Wang^*.
J. Chem. Inf. Model. 2024, 64, 6, 1892–1906.
[PDF] [Code]
A Robust Induced Fit Docking Approach with the Combination of the Hybrid All-Atom/United-Atom/Coarse-Grained Model and Simulated Annealing
Dexin Lu，Ding Luo，Yuwei Zhang*，Binju Wang^*.
J. Chem. Theory Comput. 2024, 20, 14, 6414–6423.
[PDF]

Molecular simulations

Computational strategies towards developing novel SARS-CoV-2 Mpro inhibitors against COVID-19
Ding Luo, Jian-Bo Tong^*, Xing Zhang, Xue-Chun Xiao, Shuai Bian.
J. Mol. Struct. 2022, 1247, 131378.
[PDF]
Theoretically exploring selective-binding mechanisms of BRD4 through integrative computational approaches
Ding Luo, Jian-Bo Tong^*, Xuechun Xiao, Shuai Bian, Xing Zhang, Jie Wang, Hai-Yin Xu.
SAR QSAR Environ. Res. 2021, 32, 12, 985-1011.
[PDF]
3D-QSAR and Molecular Docking Analysis for Natural Aurone Derivatives as Anti-Malarial Agents
Ding Luo, Jian-Bo Tong^*, Yi Feng.
Polycycl. Aromat. Comp. 2021, 42,6017-6032.
[PDF]