HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA. - Gaoqi Weng; Ercheng Wang; Zhe Wang 041; Hui Liu; Feng Zhu 004; Dan Li 013; Tingjun Hou (Nucleic Acids Res., 2019)

Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities. - Ercheng Wang; Hui Liu; Junmei Wang; Gaoqi Weng; Huiyong Sun; Zhe Wang 041; Yu Kang 002; Tingjun Hou (J. Chem. Inf. Model., 2020)

Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening? - Chao Shen 008; Gaoqi Weng; Xujun Zhang; Elaine Lai-Han Leung; Xiaojun Yao; Jinping Pang; Xin Chai; Dan Li 013; Ercheng Wang; Dong-Sheng Cao 001; Tingjun Hou (Briefings Bioinform., 2021)

ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions. - Xujun Zhang; Chao Shen 008; Xueying Guo; Zhe Wang 041; Gaoqi Weng; Qing Ye; Gaoang Wang; Qiaojun He; Bo Yang 023; Dong-Sheng Cao 001; Tingjun Hou (J. Cheminformatics, 2021)

VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein-Ligand Binding Free Energy Calculations. - Ercheng Wang; Weitao Fu; Dejun Jiang 002; Huiyong Sun; Junmei Wang; Xujun Zhang; Gaoqi Weng; Hui Liu; Peng Tao 007; Tingjun Hou (J. Chem. Inf. Model., 2021)

CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors. - Hongyan Du; Junbo Gao; Gaoqi Weng; Jun-Jie Ding; Xin Chai; Jinping Pang; Yu Kang 002; Dan Li 013; Dong-Sheng Cao 001; Tingjun Hou (Nucleic Acids Res., 2021)

PROTAC-DB: an online database of PROTACs. - Gaoqi Weng; Chao Shen 008; Dong-Sheng Cao 001; Junbo Gao; Xiaowu Dong; Qiaojun He; Bo Yang 023; Dan Li 013; Jian Wu 001; Tingjun Hou (Nucleic Acids Res., 2021)

ReMODE: a deep learning-based web server for target-specific drug design. - Mingyang Wang 004; Jike Wang; Gaoqi Weng; Yu Kang 002; Peichen Pan; Dan Li 013; Yafeng Deng; Honglin Li 003; Chang-Yu Hsieh; Tingjun Hou (J. Cheminformatics, 2022)

Learning on topological surface and geometric structure for 3D molecular generation. - Odin Zhang; Tianyue Wang; Gaoqi Weng; Dejun Jiang 002; Ning Wang; Xiaorui Wang; Huifeng Zhao; Jialu Wu; Ercheng Wang; Guangyong Chen; Yafeng Deng; Peichen Pan; et al. (Nat. Comput. Sci., 2023)

PROTAC-DB 2.0: an updated database of PROTACs. - Gaoqi Weng; Xuanyan Cai; Dong-Sheng Cao 001; Hongyan Du; Chao Shen 008; Yafeng Deng; Qiaojun He; Bo Yang 023; Dan Li 013; Tingjun Hou (Nucleic Acids Res., 2023)

Genetic Algorithm-Based Receptor Ligand: A Genetic Algorithm-Guided Generative Model to Boost the Novelty and Drug-Likeness of Molecules in a Sampling Chemical Space. - Mingyang Wang 004; Zhengjian Wu; Jike Wang; Gaoqi Weng; Yu Kang 002; Peichen Pan; Dan Li 013; Yafeng Deng; Xiaojun Yao; Zhitong Bing; Chang-Yu Hsieh; Tingjun Hou (J. Chem. Inf. Model., 2024)

Durian: A Comprehensive Benchmark for Structure-Based 3D Molecular Generation. - Dou Nie; Huifeng Zhao; Odin Zhang; Gaoqi Weng; Hui Zhang; Jieyu Jin; Haitao Lin; Yufei Huang 002; Liwei Liu; Dan Li 013; Tingjun Hou; Yu Kang 002 (J. Chem. Inf. Model., 2025)