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2025
Conflitti P.; Lyman E.; Sansom M. et al., Functional dynamics of G protein-coupled receptors reveal new routes for drug discovery. Nature Review Drug Discovery 2025


2024
Li, H.; Sun, X.; Cui, W.; Xu, M.; Dong J.; Ekundayo, BE; Ni, D.; Rao, Z.; Guo, L.; Stahlberg,H.*; Yuan, S.*; Vogel, H.*, Computational drug development for membrane protein targets. Nature Biotechnology 2024.

Wu, C.; Xu. M.; Dong, J.; Cui, W.; Yuan, S.*, The structure and function of olfactory receptors. Trends in Pharm Sci 2024.

Dong, J.; Wang, S.; Cui, W.; Sun, X.; Guo, H.; Yan H.; Vogel H.; Wang Z.*; Yuan, S.*, Machine learning deciphered molecular mechanistics with accurate kinetic and thermodynamic prediction. Journal of Chemical Theory and Computation 2024.

Zhang Q.; Dong J.; Zhou C., Zhang D.; Yuan, S.;, Kramer D.; Xue D.; Peng C.; Machine learning for data-driven design of high-safety lithium metal anode. STAR protocols 2024, 5 (1), 102834

Cui B.; Pan Q.; Cui W.; Wang Y.; Yuan, S.; Loake G.*; Liu F.* S-nitrosylation of a cytoplasmic receptor-like kinase regulates plant immunity. Science Advances 2024

Liu C.; Cui W.; et al. Inhibitor screening for volume-sensitive LRRC8A chloride channel. Journal of Biomolecular Structure and Dynamics 2024


2023
Cui, W.; Yuan, S.*, Will the hype of automated drug discovery finally be realized?. Expert Opinion on Drug Discovery 2023.

Yuan, Z.; Wang J.; Qu Q.; Zhu Z.; Xu M.; Zhao M.; Sun C.; Peng H.; Huang X.; Dong C.; Yuan, S.*; Li, Y.*, Celastrol Combats Methicillin-Resistant Staphylococcus aureus by Targeting Δ1-Pyrroline-5-Carboxylate Dehydrogenase. Advanced Science 2023.

Ma, T.; Wang, L.; Chai, A.; Liu, C.; Cui, W.; Yuan, S.; Wing Ngor Au, S.; Sun, L.; Zhang, X.; Zhang, Z.; Lu, J.; Gao, Y.; Wang, P.; Li, Z.; Liang, Y.; Vogel, H.*; Wang, Y. T.*; Wang, D.*; Yan, K.*; Zhang, H.*, Cryo-EM structures of ClC-2 chloride channel reveal the blocking mechanism of its specific inhibitor AK-42. Nat Commun 2023, 14 (1), 3424.

Zhang, H.; Wang, S.; Zhang, Z.; Hou, M.; Du, C.; Zhao, Z.; Vogel, H.; Li, Z.; Yan, K.; Zhang, X.; Lu, J.; Liang, Y.; Yuan, S.*; Wang, D.*; Zhang, H.*, Cryo-EM structure of human heptameric pannexin 2 channel. Nat Commun 2023, 14 (1), 1118.

Qu, Q.; Cui, W.; Huang, X.; Zhu, Z.; Dong, Y.; Yuan, Z.; Dong, C.; Zheng, Y.; Chen, X.; Yuan, S.*; Li, Y.*, Gallic Acid Restores the Sulfonamide Sensitivity of Multidrug-Resistant Streptococcus suis via Polypharmaceology Mechanism. J Agric Food Chem 2023, 71 (18), 6894-6907.

Cui, W.; Dong, J.; Wang, S.; Vogel, H.; Zou, R.; Yuan, S.*, Molecular basis of ligand selectivity for melatonin receptors. RSC Adv 2023, 13 (7), 4422-4430.


2022
Xu, M.; li, Y.; Dong, J.; Yuan, S.*, GPCR-IFP: A Web Server for Analyzing G-Protein Coupled ReceptorLigand Fingerprint Interaction from Experimental Structures. bioxrix 2022.

Xing, C.; Cui, W. Q.; Zhang, Y.; Zou, X. S.; Hao, J. Y.; Zheng, S. D.; Wang, T. T.; Wang, X. Z.; Wu, T.; Liu, Y. Y.; Chen, X. Y.; Yuan, S.* G.; Zhang, Z. Y.*; Li, Y. H.*, Ultrasound-assisted deep eutectic solvents extraction of glabridin and isoliquiritigenin from Glycyrrhiza glabra: Optimization, extraction mechanism and in vitro bioactivities. Ultrason Sonochem 2022, 83, 105946.

Wang, X.; Yuan, S.*; Chan, H. C. S.*, Translocation Mechanism of Allosteric Sodium Ions in beta(2)-Adrenoceptor. J Chem Inf Model 2022, 62 (12), 3090-3095.

Wang, S.; Sun, X.; Cui, W.; Yuan, S.*, MM/PB(GB)SA benchmarks on soluble proteins and membrane proteins. Front Pharmacol 2022, 13, 1018351.

Wang, H.; Wang, S.; Wang, J.; Shen, X.; Feng, X.; Yuan, S.; Sun, X.; Yuan, Q., Engineering a Prokaryotic Non-P450 Hydroxylase for 3'-Hydroxylation of Flavonoids. ACS Synth Biol 2022, 11 (11), 3865-3873.

Lan, D.; Li, S.; Tang, W.; Zhao, Z.; Luo, M.; Yuan, S.*; Xu, J.; Wang*, Y., Glycerol is Released from a New Path in MGL Lipase Catalytic Process. J Chem Inf Model 2022, 62 (9), 2248-2256.

Hou, Y.; Wang, S.; Bai, B.; Chan, H. C. S.*; Yuan, S.*, Accurate Physical Property Predictions via Deep Learning. Molecules 2022, 27 (5).

Chen, M.; Li, Y.; Li, S.; Cui, W.; Zhou, Y.; Qu, Q.; Che, R.; Li, L.; Yuan, S.*; Liu, X.*, Molecular Mechanism of Staphylococcus xylosus Resistance Against Tylosin and Florfenicol. Infect Drug Resist 2022, 15, 6165-6176.


2021
Zou, R.; Wang, X.; Li, S.; Chan, H. C. S.; Vogel, H.; Yuan, S.*, The role of metal ions in G protein‐coupled receptor signalling and drug discovery. WIREs Computational Molecular Science 2021, 12 (2).

Yao, D.; Wang, Y.; Zou, R.; Bian, K.; Yuan, S.*; Zhang, B.*; Wang, D.*, Wavelength-adjustable butterfly molecules in dynamic nanoassemblies for Extradomain-B fibronectin-modulating optical imaging and synchronous phototherapy of triple-negative breast cancer. Chemical Engineering Journal 2021, 420.

Xia, Y.; Zou, R.; Escouboue, M.; Zhong, L.; Zhu, C.; Pouzet, C.; Wu, X.; Wang, Y.; Lv, G.; Zhou, H.; Sun, P.; Ding, K.; Deslandes, L.; Yuan, S.*; Zhang, Z. M.*, Secondary-structure switch regulates the substrate binding of a YopJ family acetyltransferase. Nat Commun 2021, 12 (1), 5969.

Lan, D.; Zhao, G.; Holzmann, N.; Yuan, S.*; Wang, J.*; Wang, Y.*, Structure-Guided Rational Design of a Mono- and Diacylglycerol Lipase from Aspergillus oryzae: A Single Residue Mutant Increases the Hydrolysis Ability. J Agric Food Chem 2021, 69 (18), 5344-5352.

Cui, W.; Yu, F.; Zhang, Y.; Han, X.; Zou, R.; Tang, Y.; Wang, L.; Eliphaz, N.; Wang, J.; Yuan, S.*; Cai, X.; Li, Y., Discovery of traditional Chinese medicines against porcine reproductive and respiratory syndrome virus. Pharmacological Research - Modern Chinese Medicine 2021, 1.

Bai, B.; Zou, R.; Chan, H. C. S.; Li, H.*; Yuan, S.*, MolADI: A Web Server for Automatic Analysis of Protein-Small Molecule Dynamic Interactions. Molecules 2021, 26 (15).


2020
Liu, K.; Zou, R.; Cui, W.; Li, M.; Wang, X.; Dong, J.; Li, H.; Li, H.; Wang, P.; Shao, X.; Su, W.; Chan, H. C. S.; Li, H.; Yuan, S.*, Clinical HDAC Inhibitors Are Effective Drugs to Prevent the Entry of SARS-CoV2. ACS Pharmacol Transl Sci 2020, 3 (6), 1361-1370.

Liu, K.; Wu, L.; Yuan, S.; Wu, M.; Xu, Y.; Sun, Q.; Li, S.; Zhao, S.; Hua, T.; Liu, Z. J., Structural basis of CXC chemokine receptor 2 activation and signalling. Nature 2020, 585 (7823), 135-140.

Hua, T.; Li, X.; Wu, L.; Iliopoulos-Tsoutsouvas, C.; Wang, Y.; Wu, M.; Shen, L.; Brust, C. A.; Nikas, S. P.; Song, F.; Song, X.; Yuan, S.; Sun, Q.; Wu, Y.; Jiang, S.; Grim, T. W.; Benchama, O.; Stahl, E. L.; Zvonok, N.; Zhao, S.; Bohn, L. M.; Makriyannis, A.; Liu, Z.-J., Activation and Signaling Mechanism Revealed by Cannabinoid Receptor-Gi Complex Structures. Cell 2020, 180 (4), 655-665.e18.

Cui, W.; Aouidate, A.; Wang, S.; Yu, Q.; Li, Y.; Yuan, S.*, Discovering Anti-Cancer Drugs via Computational Methods. Front Pharmacol 2020, 11, 733.

Chan, H. C. S.; Xu, Y.; Tan, L.; Vogel, H.; Cheng, J.*; Wu, D.*; Yuan, S.*, Enhancing the Signaling of GPCRs via Orthosteric Ions. ACS Cent Sci 2020, 6 (2), 274-282.


2019
Zheng, L.; Falschlunger, C.; Huang, K.; Mairhofer, E.; Yuan, S.; Wang, J.; Patel, D. J.; Micura, R.; Ren, A., Hatchet ribozyme structure and implications for cleavage mechanism. Proc Natl Acad Sci U S A 2019, 116 (22), 10783-10791.

Yuan, S.*; Dahoun, T.; Brugarolas, M.; Pick, H.; Filipek, S.; Vogel, H.*, Computational modeling of the olfactory receptor Olfr73 suggests a molecular basis for low potency of olfactory receptor-activating compounds. Commun Biol 2019, 2, 141.

Liu, L.; Chan, S.; Mo, T.; Ding, W.; Yu, S.; Zhang, Q.*; Yuan, S.*, Movements of the Substrate-Binding Clamp of Cypemycin Decarboxylase CypD. J Chem Inf Model 2019, 59 (6), 2924-2929.

Chen, X.; Xu, Y.; Qu, L.; Wu, L.; Han, G. W.; Guo, Y.; Wu, Y.; Zhou, Q.; Sun, Q.; Chu, C.; Yang, J.; Yang, L.; Wang, Q.; Yuan, S.; Wang, L.; Hu, T.; Tao, H.; Sun, Y.; Song, Y.; Hu, L.; Liu, Z. J.; Stevens, R. C.; Zhao, S.; Wu, D.; Zhong, G., Molecular Mechanism for Ligand Recognition and Subtype Selectivity of alpha(2C) Adrenergic Receptor. Cell Rep 2019, 29 (10), 2936-2943 e4.

Chan, H. C. S.; Shan, H.; Dahoun, T.; Vogel, H.; Yuan, S.*, Advancing Drug Discovery via Artificial Intelligence. Trends Pharmacol Sci 2019, 40 (8), 592-604.

Chan, H. C. S.; Li, Y.; Dahoun, T.; Vogel, H.; Yuan, S.*, New Binding Sites, New Opportunities for GPCR Drug Discovery. Trends Biochem Sci 2019, 44 (4), 312-330.


2018
Zhou, Y.; Li, W.; You, W.; Di, Z.; Wang, M.; Zhou, H.; Yuan, S.; Wong, N. K.; Xiao, Y., Discovery of Arabidopsis UGT73C1 as a steviol-catalyzing UDP-glycosyltransferase with chemical probes. Chem Commun (Camb) 2018, 54 (52), 7179-7182.

Yan, Y.; Liu, Q.; Zang, X.; Yuan, S.; Bat-Erdene, U.; Nguyen, C.; Gan, J.; Zhou, J.; Jacobsen, S. E.; Tang, Y., Resistance-gene-directed discovery of a natural-product herbicide with a new mode of action. Nature 2018, 559 (7714), 415-418.

Sun, Z.; Wu, L.; Bocola, M.; Chan, H. C. S.; Lonsdale, R.; Kong, X. D.; Yuan, S.*; Zhou, J.*; Reetz, M. T.*, Structural and Computational Insight into the Catalytic Mechanism of Limonene Epoxide Hydrolase Mutants in Stereoselective Transformations. J Am Chem Soc 2018, 140 (1), 310-318.

Peng, Y.; McCorvy, J. D.; Harpsoe, K.; Lansu, K.; Yuan, S.; Popov, P.; Qu, L.; Pu, M.; Che, T.; Nikolajsen, L. F.; Huang, X. P.; Wu, Y.; Shen, L.; Bjorn-Yoshimoto, W. E.; Ding, K.; Wacker, D.; Han, G. W.; Cheng, J.; Katritch, V.; Jensen, A. A.; Hanson, M. A.; Zhao, S.; Gloriam, D. E.; Roth, B. L.; Stevens, R. C.; Liu, Z. J., 5-HT(2C) Receptor Structures Reveal the Structural Basis of GPCR Polypharmacology. Cell 2018, 172 (4), 719-730 e14.

Li, W.; Zhou, Y.; You, W.; Yang, M.; Ma, Y.; Wang, M.; Wang, Y.; Yuan, S.; Xiao, Y., Development of Photoaffinity Probe for the Discovery of Steviol Glycosides Biosynthesis Pathway in Stevia rebuadiana and Rapid Substrate Screening. ACS Chem Biol 2018, 13 (8), 1944-1949.

Ernst, I.; Haase, M.; Ernst, S.; Yuan, S.; Kuhn, A.; Leptihn, S., Large conformational changes of a highly dynamic pre-protein binding domain in SecA. Commun Biol 2018, 1, 130.

Chan, H. C. S.; Wang, J.; Palczewski, K.; Filipek, S.; Vogel, H.; Liu, Z. J.; Yuan, S.*, Exploring a new ligand binding site of G protein-coupled receptors. Chem Sci 2018, 9 (31), 6480-6489.

Chan, H. C. S.; Pan, L.; Li, Y.; Yuan, S.*, Rationalization of stereoselectivity in enzyme reactions. WIREs Computational Molecular Science 2018, 9 (4).


2017
Yuan, S.*; Chan, H. C. S.; Hu, Z., Using PyMOL as a platform for computational drug design. WIREs Computational Molecular Science 2017, 7 (2), e1298.

Yuan, S.*; Chan, H. C. S.; Hu, Z., Implementing WebGL and HTML5 in Macromolecular Visualization and Modern Computer-Aided Drug Design. Trends Biotechnol 2017, 35 (6), 559-571.

Yuan, H.; Zhang, J.; Cai, Y.; Wu, S.; Yang, K.; Chan, H. C. S.; Huang, W.; Jin, W. B.; Li, Y.; Yin, Y.; Igarashi, Y.; Yuan, S.*; Zhou, J.*; Tang, G. L.*, GyrI-like proteins catalyze cyclopropanoid hydrolysis to confer cellular protection. Nat Commun 2017, 8 (1), 1485.

Wang, J. B.; Ilie, A.; Yuan, S.*; Reetz, M. T.*, Investigating Substrate Scope and Enantioselectivity of a Defluorinase by a Stereochemical Probe. J Am Chem Soc 2017, 139 (32), 11241-11247.

Chan, H. C. S.; McCarthy, D.; Li, J.; Palczewski, K.*; Yuan, S.*, Designing Safer Analgesics via mu-Opioid Receptor Pathways. Trends Pharmacol Sci 2017, 38 (11), 1016-1037.


2016
Zhang, Z. M.; Ma, K. W.; Yuan, S.; Luo, Y.; Jiang, S.; Hawara, E.; Pan, S.; Ma, W.; Song, J., Structure of a pathogen effector reveals the enzymatic mechanism of a novel acetyltransferase family. Nat Struct Mol Biol 2016, 23 (9), 847-52.

Yuan, S.*; Peng, Q.; Palczewski, K.; Vogel, H.; Filipek, S., Mechanistic Studies on the Stereoselectivity of the Serotonin 5-HT1A Receptor. Angew Chem Int Ed Engl 2016, 55 (30), 8661-5.

Yuan, S.*; Filipek, S.; Vogel, H., A Gating Mechanism of the Serotonin 5-HT3 Receptor. Structure 2016, 24 (5), 816-825.

Yuan, S.*; Chan, H. C. S.; Filipek, S.; Vogel, H., PyMOL and Inkscape Bridge the Data and the Data Visualization. Structure 2016, 24 (12), 2041-2042.

Yuan, S.*; Chan, H. C.; Vogel, H.; Filipek, S.; Stevens, R. C.; Palczewski, K., The Molecular Mechanism of P2Y1 Receptor Activation. Angew Chem Int Ed Engl 2016, 55 (35), 10331-5.

Ji, X.; Liu, W. Q.; Yuan, S.; Yin, Y.; Ding, W.; Zhang, Q., Mechanistic study of the radical SAM-dependent amine dehydrogenation reactions. Chem Commun (Camb) 2016, 52 (69), 10555-8.

Chan, H. C.; Filipek, S.; Yuan, S.*, The Principles of Ligand Specificity on beta-2-adrenergic receptor. Sci Rep 2016, 6, 34736.


2015
Yuan, S.*; Palczewski, K.; Peng, Q.; Kolinski, M.; Vogel, H.; Filipek, S., The mechanism of ligand-induced activation or inhibition of mu- and kappa-opioid receptors. Angew Chem Int Ed Engl 2015, 54 (26), 7560-3.

Yuan, S.*; Hu, Z.; Filipek, S.; Vogel, H., W246(6.48) opens a gate for a continuous intrinsic water pathway during activation of the adenosine A2A receptor. Angew Chem Int Ed Engl 2015, 54 (2), 556-9.

Baud, O.#; Yuan, S.#; Veya, L.; Filipek, S.; Vogel, H.; Pick, H.*, Exchanging ligand-binding specificity between a pair of mouse olfactory receptor paralogs reveals odorant recognition principles. Sci Rep 2015, 5, 14948.


2014
Yuan, S.*; Filipek, S.; Palczewski, K.; Vogel, H.*, Activation of G-protein-coupled receptors correlates with the formation of a continuous internal water pathway. Nat Commun 2014, 5, 4733.

Kufareva, I.; Katritch, V.; Participants of, G. D.; Stevens, R. C.; Abagyan, R., Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure 2014, 22 (8), 1120-1139.

Kong, X. D.; Yuan, S.; Li, L.; Chen, S.; Xu, J. H.; Zhou, J., Engineering of an epoxide hydrolase for efficient bioresolution of bulky pharmaco substrates. Proc Natl Acad Sci U S A 2014, 111 (44), 15717-22.


2013
Yuan, S.*; Vogel, H.; Filipek, S.*, The role of water and sodium ions in the activation of the mu-opioid receptor. Angew Chem Int Ed Engl 2013, 52 (38), 10112-5.

Yuan, S.*; Wu, R.; Latek, D.; Trzaskowski, B.; Filipek, S.*, Lipid receptor S1P(1) activation scheme concluded from microsecond all-atom molecular dynamics simulations. PLoS Comput Biol 2013, 9 (10), e1003261.

Wu, Y.; Yuan, S.; Chen, S.; Wu, D.; Chen, J.; Wu, J., Enhancing the production of galacto-oligosaccharides by mutagenesis of Sulfolobus solfataricus beta-galactosidase. Food Chem 2013, 138 (2-3), 1588-95.


before 2013
Le Roy, K.; Vergauwen, R.; Struyf, T.; Yuan, S.; Lammens, W.; Matrai, J.; De Maeyer, M.; Van den Ende, W., Understanding the role of defective invertases in plants: tobacco Nin88 fails to degrade sucrose. Plant Physiol 2013, 161 (4), 1670-81.

Yuan, S.; Le Roy, K.; Venken, T.; Lammens, W.; Van den Ende, W.; De Maeyer, M., pKa modulation of the acid/base catalyst within GH32 and GH68: a role in substrate/inhibitor specificity? PLoS One 2012, 7 (5), e37453.

Yuan, S.; Ghoshdastider, U.; Trzaskowski, B.; Latek, D.; Debinski, A.; Pulawski, W.; Wu, R.; Gerke, V.; Filipek, S., The role of water in activation mechanism of human N-formyl peptide receptor 1 (FPR1) based on molecular dynamics simulations. PLoS One 2012, 7 (11), e47114.

Trzaskowski, B.; Latek, D.; Yuan, S.; Ghoshdastider, U.; Debinski, A.; Filipek, S., Action of molecular switches in GPCRs--theoretical and experimental studies. Curr Med Chem 2012, 19 (8), 1090-109.

Lammens, W.; Le Roy, K.; Yuan, S.; Vergauwen, R.; Rabijns, A.; Van Laere, A.; Strelkov, S. V.; Van den Ende, W., Crystal structure of 6-SST/6-SFT from Pachysandra terminalis, a plant fructan biosynthesizing enzyme in complex with its acceptor substrate 6-kestose. Plant J 2012, 70 (2), 205-19.

Zheng, C.; Liu, H. H.; Yuan, S.; Zhou, J.; Zhang, B., Molecular basis of LMAN1 in coordinating LMAN1-MCFD2 cargo receptor formation and ER-to-Golgi transport of FV/FVIII. Blood 2010, 116 (25), 5698-706.