Increasing the time step with mass scaling in Born-Oppenheimer ab initio QM/MM molecular dynamics simulations. - Han Zheng; Shenglong Wang; Yingkai Zhang (J. Comput. Chem., 2009)

Performance analysis of user association policies in small cell networks using Stochastic Petri Nets. - Yingkai Zhang; Lei Lei 004; Hang Long; Kan Zheng (ICC Workshops, 2013)

Performance Analysis of Device-to-Device Communications with Dynamic Interference Using Stochastic Petri Nets. - Lei Lei 004; Yingkai Zhang; Xuemin (Sherman) Shen; Chuang Lin 002; Zhangdui Zhong (IEEE Trans. Wirel. Commun., 2013)

Performance Analysis and Evaluation of Deployment in Small Cell Networks. - Kan Zheng; Yue Li; Yingkai Zhang; Zheng Jiang; Hang Long (KSII Trans. Internet Inf. Syst., 2015)

Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An Ab initio QM/MM molecular dynamics study. - Wenjing Gong; Ruibo Wu; Yingkai Zhang (J. Comput. Chem., 2015)

AlphaSpace: Fragment-Centric Topographical Mapping To Target Protein-Protein Interaction Interfaces. - David Rooklin; Cheng Wang; Joseph Katigbak; Paramjit S. Arora; Yingkai Zhang (J. Chem. Inf. Model., 2015)

Performance analysis of device-to-device communications underlaying cellular networks. - Wenjun Wu 002; Wei Xiang 001; Yingkai Zhang; Kan Zheng; Wenbo Wang 007 (Telecommun. Syst., 2015)

Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest. - Cheng Wang; Yingkai Zhang (J. Comput. Chem., 2017)

Computational Strategy for Bound State Structure Prediction in Structure-Based Virtual Screening: A Case Study of Protein Tyrosine Phosphatase Receptor Type O Inhibitors. - Xuben Hou; David Rooklin; Duxiao Yang; Xiao Liang; Kangshuai Li; Jianing Lu; Cheng Wang; Peng Xiao; Yingkai Zhang; Jin-peng Sun; Hao Fang 006 (J. Chem. Inf. Model., 2018)

Exploring fragment-based target-specific ranking protocol with machine learning on cathepsin S. - Yuwei Yang; Jianing Lu; Chao Yang 023; Yingkai Zhang (J. Comput. Aided Mol. Des., 2019)

Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions. - Jianing Lu; Xuben Hou; Cheng Wang; Yingkai Zhang (J. Chem. Inf. Model., 2019)

AlphaSpace 2.0: Representing Concave Biomolecular Surfaces Using β-Clusters. - Joseph Katigbak; Haotian Li; David Rooklin; Yingkai Zhang (J. Chem. Inf. Model., 2020)

Dataset Construction to Explore Chemical Space with 3D Geometry and Deep Learning. - Jianing Lu; Song Xia; Jieyu Lu; Yingkai Zhang (J. Chem. Inf. Model., 2021)

Lin_F9: A Linear Empirical Scoring Function for Protein-Ligand Docking. - Chao Yang 023; Yingkai Zhang (J. Chem. Inf. Model., 2021)

Reinforcement Learning Based Plug-and-Play Method for Hyperspectral Image Reconstruction. - Ying Fu; Yingkai Zhang (CICAI (1), 2022)

CovBinderInPDB: A Structure-Based Covalent Binder Database. - Xiao-Kang Guo; Yingkai Zhang (J. Chem. Inf. Model., 2022)

Unified Deep Learning Model for Multitask Reaction Predictions with Explanation. - Jieyu Lu; Yingkai Zhang (J. Chem. Inf. Model., 2022)

Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein-Ligand Scoring Functions. - Chao Yang 023; Yingkai Zhang (J. Chem. Inf. Model., 2022)

Accurate Prediction of Aqueous Free Solvation Energies Using 3D Atomic Feature-Based Graph Neural Network with Transfer Learning. - Dongdong Zhang; Song Xia; Yingkai Zhang (J. Chem. Inf. Model., 2022)

Deciphering the Allosteric Activation Mechanism of SIRT6 Using Molecular Dynamics Simulations. - Zhiyuan Zhao; Jintong Du; Yu Du; Yuan Gao; Mingxuan Yu; Yingkai Zhang; Hao Fang 006; Xuben Hou (J. Chem. Inf. Model., 2023)

Technique Report of CVPR 2024 PBDL Challenges. - Ying Fu 001; Yu Li 003; Shaodi You; Boxin Shi; Jose Alvarez; Coert Van Gemeren; Linwei Chen; Yunhao Zou; Zichun Wang; Yichen Li; Yuze Han; Yingkai Zhang; et al. (CoRR, 2024)

TraceAwareness and dual-strategy fuzz testing: Enhancing path coverage and crash localization with stochastic science and large language models. - Xiaoquan Chen; Jian Liu; Yingkai Zhang; Qinsong Hu; Yupeng Han; Ruqi Zhang; Jingqi Ran; Lei Yan; Baiqi Huang; Shengtin Ma (Comput. Electr. Eng., 2025)

Can Deep Learning Blind Docking Methods be Used to Predict Allosteric Compounds? - Eric A. Chen; Yingkai Zhang (J. Chem. Inf. Model., 2025)

Unified Deep Learning of Molecular and Protein Language Representations with T5ProtChem. - Thomas Kelly; Song Xia; Jieyu Lu; Yingkai Zhang (J. Chem. Inf. Model., 2025)

Normalized Protein-Ligand Distance Likelihood Score for End-to-End Blind Docking and Virtual Screening. - Song Xia; Yaowen Gu; Yingkai Zhang (J. Chem. Inf. Model., 2025)

Unaligned RGB Guided Hyperspectral Image Super-Resolution with Spatial-Spectral Concordance. - Yingkai Zhang; Zeqiang Lai; Tao Zhang; Ying Fu 001; Chenghu Zhou (CoRR, 2025)