Publications by authors named "Runduo Liu"

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ALCHEMD: Bridging Accessibility and Accuracy in Automated Relative Binding Free Energy Workflows.
Runduo Liu, Yilin Zhong, Yufen Yao, Wanyi Huang, Zongda Li

J Chem Theory Comput· December 2025

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Discovery of novel azetidine-based imidazopyridines as selective and orally bioavailable inhibitors of phosphodiesterase 10A for the treatment of pulmonary arterial hypertension.
Hongzhe Huang, Huanxin Xue, Anqi Cai, Han Yuan, Yufen Yao, Runduo Liu, Ting Liu

Eur J Med Chem· June 2025

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State Function-Based Correction: A Simple and Efficient Free-Energy Correction Algorithm for Large-Scale Relative Binding Free-Energy Calculations.
Runduo Liu, Yijun Lai, Yufen Yao, Wanyi Huang, Yilin Zhong

J Phys Chem Lett· June 2025

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3D-EDiffMG: 3D equivariant diffusion-driven molecular generation to accelerate drug discovery.
Chao Xu, Runduo Liu, Yufen Yao, Wanyi Huang, Zhe Li

J Pharm Anal· June 2025

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Divide-and-Conquer ABFE: Improving Free Energy Calculations by Enhancing Water Sampling.
Runduo Liu, Yufen Yao, Wanyi Huang, Yilin Zhong, Hai-Bin Luo

J Chem Theory Comput· April 2025

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RED-E-Function-Based Equilibrium Parameter Finder: Finding the Best Restraint Parameters in Absolute Binding Free Energy Calculations.
Wanyi Huang, Runduo Liu, Yufen Yao, Yijun Lai, Hai-Bin Luo

J Phys Chem Lett· January 2025

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Molecular Dynamics-Assisted Discovery of Novel Phosphodiesterase-5 Inhibitors Targeting a Unique Allosteric Pocket.
Weihao Luo, Runduo Liu, Xinlin Cai, Qian Zhou, Chen Zhang

Molecules· January 2025

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Discovery of highly potent phosphodiesterase-1 inhibitors by a combined-structure free energy perturbation approach.
Zhe Li, Mei-Yan Jiang, Runduo Liu, Quan Wang, Qian Zhou

Acta Pharm Sin B· December 2024

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Convergence-Adaptive Roundtrip Method Enables Rapid and Accurate FEP Calculations.
Yufen Yao, Runduo Liu, Wenchao Li, Wanyi Huang, Yijun Lai

J Chem Theory Comput· September 2024

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Cryo-EM structure of small-molecule agonist bound delta opioid receptor-G complex enables discovery of biased compound.
Lin Cheng, Zhuang Miao, Sicen Liu, Zhe Li, Hong Fu, Yuxuan Liu, Wencheng Liu, Runduo Liu, Jianfeng Liu

Nat Commun· September 2024

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Targeting ATP-binding site of WRN Helicase: Identification of novel inhibitors through pocket analysis and Molecular Dynamics-Enhanced virtual screening.
Hao Yuan, Run-Duo Liu, Zhuo-Yu Gao, Li-Ting Zhong, Ying-Chen Zhou

Bioorg Med Chem Lett· May 2024

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Discovery of novel selective phosphodiesterase‑1 inhibitors for the treatment of acute myelogenous leukemia.
Mei-Ling Le, Yi-Yi Yang, Mei-Yan Jiang, Chuan Han, Zhi-Rong Guo, Run-Duo Liu

Bioorg Chem· March 2024

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Accelerating and Automating the Free Energy Perturbation Absolute Binding Free Energy Calculation with the RED-E Function.
Runduo Liu, Wenchao Li, Yufen Yao, Yinuo Wu, Hai-Bin Luo

J Chem Inf Model· December 2023

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Identification of Novel Quinolin-2(1)-ones as Phosphodiesterase 1 Inhibitors for the Treatment of Inflammatory Bowel Disease.
Bei Zhang, Yi-Yi Yang, Zheng-Jiong Zhao, Run-Duo Liu, Ling-Ling Feng

J Med Chem· September 2023

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3D-SMGE: a pipeline for scaffold-based molecular generation and evaluation.
Chao Xu, Runduo Liu, Shuheng Huang, Wenchao Li, Zhe Li

Brief Bioinform· September 2023

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An Open Source Graph-Based Weighted Cycle Closure Method for Relative Binding Free Energy Calculations.
Yishui Li, Runduo Liu, Jie Liu, Haibin Luo, Chengkun Wu

J Chem Inf Model· January 2023

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Free energy perturbation-based large-scale virtual screening for effective drug discovery against COVID-19.
Zhe Li, Chengkun Wu, Yishui Li, Runduo Liu, Kai Lu, Jie Liu

Int J High Perform Comput Appl· January 2023

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Computer simulation and design of DNA-nanoprobe for fluorescence imaging DNA repair enzyme in living cells.
Cheng Tian, Guangzhong Liang, Chunyi Wang, Ruikai He, Keni Ning, Runduo Liu

Biosens Bioelectron· September 2022

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Structural Modifications of Nimodipine Lead to Novel PDE1 Inhibitors with Anti-pulmonary Fibrosis Effects.
Meng-Xing Huang, Yi-Jing Tian, Chuan Han, Run-Duo Liu, Xi Xie

J Med Chem· June 2022

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Discovery of Dipyridamole Analogues with Enhanced Metabolic Stability for the Treatment of Idiopathic Pulmonary Fibrosis.
Meng-Xing Huang, Yan-Quan Chen, Run-Duo Liu, Yue Huang, Chen Zhang

Molecules· May 2022

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Free energy perturbation (FEP)-guided scaffold hopping.
Deyan Wu, Xuehua Zheng, Runduo Liu, Zhe Li, Zan Jiang

Acta Pharm Sin B· March 2022

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Reply to Behnam and Klein: Potential role of the His-tag in C-terminal His-tagged SARS-CoV-2 main protease.
Zhe Li, Runduo Liu, Chang-Guo Zhan, Xin Wang, Hai-Bin Luo

Proc Natl Acad Sci U S A· September 2021

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Discovery of Highly Specific Catalytic-Site-Targeting Fluorescent Probes for Detecting Lysosomal PDE10A in Living Cells.
Yuqi Gao, Ju Huang, Qian Zhou, Runduo Liu, Sirui Zhang

ACS Chem Biol· May 2021

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Reply to Ma and Wang: Reliability of various in vitro activity assays on SARS-CoV-2 main protease inhibitors.
Zhe Li, Yuxi Lin, Yi-You Huang, Runduo Liu, Chang-Guo Zhan

Proc Natl Acad Sci U S A· February 2021

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Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs.
Zhe Li, Xin Li, Yi-You Huang, Yaoxing Wu, Runduo Liu, Hao Liu

Proc Natl Acad Sci U S A· November 2020

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