Aggregation mechanism investigation of the GIFQINS cross-beta amyloid fibril. - Hai-Feng Chen (Comput. Biol. Chem., 2009)

Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins. - Wei Ye; Dingjue Ji; Wei Wang; Ray Luo 001; Hai-Feng Chen (J. Chem. Inf. Model., 2015)

Synergistic Allosteric Mechanism of Fructose-1, 6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis. - Jingxu Yang; Hao Liu 081; Xiaorui Liu; Chengbo Gu; Ray Luo 001; Hai-Feng Chen (J. Chem. Inf. Model., 2016)

The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins. - Dong Song; Ray Luo 001; Hai-Feng Chen (J. Chem. Inf. Model., 2017)

Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations. - Wei Ye; Tianle Qian; Hao Liu 081; Ray Luo 001; Hai-Feng Chen (J. Chem. Inf. Model., 2017)

Inhibitory mechanism of 5-bromo-3-indoleacetic acid for non-structural-3 helicase hepatitis C virus with dynamics correlation network analysis. - Mueed Ur Rahman; Ashfaq Ur Rehman; Hao Liu 081; Hai-Feng Chen (Comput. Biol. Chem., 2018)

Dynamical important residue network (DIRN): network inference via conformational change. - Quan Li; Ray Luo 001; Hai-Feng Chen (Bioinform., 2019)

Exploring the Pyrazinamide Drug Resistance Mechanism of Clinical Mutants T370P and W403G in Ribosomal Protein S1 ofMycobacterium tuberculosis. - Ashfaq Ur Rehman; Muhammad Tahir Khan; Hao Liu 081; Abdul Wadood; Shaukat Iqbal Malik; Hai-Feng Chen (J. Chem. Inf. Model., 2019)

Gain-of-Function SHP2 E76Q Mutant Rescuing Autoinhibition Mechanism Associated with Juvenile Myelomonocytic Leukemia. - Ashfaq Ur Rehman; Humaira Rafiq; Mueed Ur Rahman; Jiayi Li; Hao Liu 081; Shenggan Luo; Taaha Arshad; Abdul Wadood; Hai-Feng Chen (J. Chem. Inf. Model., 2019)

Residue-Specific Force Field Improving the Sample of Intrinsically Disordered Proteins and Folded Proteins. - Sheng Yang; Hao Liu 081; Yangpeng Zhang; Hui Lu 004; Hai-Feng Chen (J. Chem. Inf. Model., 2019)

Comparison and Evaluation of Force Fields for Intrinsically Disordered Proteins. - Mueed Ur Rahman; Ashfaq Ur Rehman; Hao Liu 081; Hai-Feng Chen (J. Chem. Inf. Model., 2020)

Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins. - Dong Song; Hao Liu 081; Ray Luo 001; Hai-Feng Chen (J. Chem. Inf. Model., 2020)

Recent Force Field Strategies for Intrinsically Disordered Proteins. - Junxi Mu; Hao Liu 081; Jian Zhang 037; Ray Luo 001; Hai-Feng Chen (J. Chem. Inf. Model., 2021)

Balanced Solvent Model for Intrinsically Disordered and Ordered Proteins. - Junxi Mu; Zhengsong Pan; Hai-Feng Chen (J. Chem. Inf. Model., 2021)

RNA-Specific Force Field Optimization with CMAP and Reweighting. - Jun Chen; Hao Liu 081; Xiaochen Cui; Zhengxin Li; Hai-Feng Chen (J. Chem. Inf. Model., 2022)

Polarizable Force Field of Intrinsically Disordered Proteins with CMAP and Reweighting Optimization. - Xiaochen Cui; Hao Liu 081; Hai-Feng Chen (J. Chem. Inf. Model., 2022)

Development and Application of Offshore Trade Authenticity Verification Platform Based on Blockchain. - Hai-Feng Chen; Lv Zhang; Shuai Wang; Shan-Shan Shi (DSIE, 2023)

Personal Precise Force Field for Intrinsically Disordered and Ordered Proteins Based on Deep Learning. - Xiaoyue Ji; Hao Liu 081; Yangpeng Zhang; Jun Chen; Hai-Feng Chen (J. Chem. Inf. Model., 2023)

PTMint database of experimentally verified PTM regulation on protein-protein interaction. - Xiaokun Hong; Ningshan Li; Jiyang Lv; Yan Zhang 124; Jing Li 107; Jian Zhang 037; Hai-Feng Chen (Bioinform., 2023)

Phosphorylation Regulation Mechanism of β2 Integrin for the Binding of Filamin Revealed by Markov State Model. - Xiaokun Hong; Kaiyuan Song; Mueed Ur Rahman; Ting Wei; Yan Zhang 124; Lin-Tai Da; Hai-Feng Chen (J. Chem. Inf. Model., 2023)

Phosphorylation Modification Force Field FB18CMAP Improving Conformation Sampling of Phosphoproteins. - Ge Song; Bozitao Zhong; Bo Zhang; Ashfaq Ur Rehman; Hai-Feng Chen (J. Chem. Inf. Model., 2023)

Research and Evaluation of the Allosteric Protein-Specific Force Field Based on a Pre-Training Deep Learning Model. - Xiaoyue Ji; Xiaochen Cui; Zhengxin Li; Taeyoung Choi; Ying Wang; Wen Xiao; Yunshuo Zhao; Jinyin Zha; Jian Zhang 037; Hai-Feng Chen; Zhengtian Yu (J. Chem. Inf. Model., 2023)

Phanto-IDP: compact model for precise intrinsically disordered protein backbone generation and enhanced sampling. - Junjie Zhu; Zhengxin Li; Haowei Tong; Zhouyu Lu; Ningjie Zhang; Ting Wei; Hai-Feng Chen (Briefings Bioinform., 2023)

Graphormer supervised de novo protein design method and function validation. - Junxi Mu; Zhengxin Li; Bo Zhang; Qi Zhang; Jamshed Iqbal; Abdul Wadood; Ting Wei; Yan Feng; Hai-Feng Chen (Briefings Bioinform., 2024)

Early Aggregation Mechanism of SOD128-38 Based on Force Field Parameter of 5-Cyano-Tryptophan. - Mueed Ur Rahman; Saira Bano; Xiaokun Hong; Ruo-Xu Gu; Hai-Feng Chen (J. Chem. Inf. Model., 2024)

Multi-indicator comparative evaluation for deep learning-based protein sequence design methods. - Jinyu Yu; Junxi Mu; Ting Wei; Hai-Feng Chen (Bioinform., 2024)

Personalized Energy Adaptation through Reweighting Learning (PEARL) Force Field for Intrinsically Disordered Proteins. - Xiaoyue Ji; Junjie Zhu; Bozitao Zhong; Zhengxin Li; Taeyoung Choi; Xiaochen Cui; Ting Wei; Hai-Feng Chen (J. Chem. Inf. Model., 2025)

Nonbonded Parameter Optimization Improving Simulation of Intrinsically Disordered Phosphoproteins. - Xinyao Zheng; Ge Song; Zhengxin Li; Bowen Duan; Bofan Zhu; Hai-Feng Chen (J. Chem. Inf. Model., 2025)

MotifBench: A standardized protein design benchmark for motif-scaffolding problems. - Zhuoqi Zheng; Bo Zhang; Kieran Didi; Kevin K. Yang; Jason Yim; Joseph L. Watson; Hai-Feng Chen; Brian L. Trippe (CoRR, 2025)