Wang S, Lin T, Peng T, Xing E, Chen S, Kara LB, Cheng X*. TopMT-GAN: a 3D topology-driven generative model for efficient and diverse structure-based ligand design. Chem Sci. 2025, 16(6):2796-2809.
Purohit A, Cheng X*. Absolute and relative binding free energy calculations of nucleotides to multiple protein classes. J Chem Theory Comput. 2025, 21(4):2067-2078.
Chen S, Lin T, Basu R, Ritchey J, Wang S, Luo Y, Li X, Pei D, Kara LB, Cheng X*. Design of target specific peptide inhibitors using generative deep learning and molecular dynamics simulations. Nat Comm. 2024, 15(1):1611.
Li Z, Chan KC, Nickels JD, Cheng X*. Molecular Dynamics Refinement of Open State Serotonin 5-HT3A Receptor Structures. J Chem Inf Model. 2023, 63, 1196
Yang R, Wu S, Wang S, Rubino G, Nickels JD, Cheng X*. Refinement of SARS-CoV-2 envelope protein structure in a native-like environment by molecular dynamics simulations. Front Mol Biosci. 2022, 9, 1027223
Li Z, Chan KC, Nickels JD, Cheng X*. Electrostatic Contributions to the Binding Free Energy of Nicotine to the Acetylcholine Binding Protein. J Phys Chem B. 2022, 126(43):8669-79
Cheng C, Geng F, Li Z, Cheng X, Zhong Y, Zhao Y, Mo X, Horbinski C, Duan W, Chakravarti A, Cheng X, Guo D. Ammonia is a key signaling molecule activating SREBP-1 and lipogenesis to promote tumor growth. Nat Metab. 2022, 4, 575-588
Wang Z, Huang W, Liu M, Kennel SJ, Wall JS, Cheng X*. Computational investigation of the binding of a designed peptide to λ light chain amyloid fibril. Phys Chem Chem Phys. 2021, 23 (36), 20634-20644
Kong X, Xing E, Zhuang T, Li PK, Cheng X*. Mechanistic Insights into the Allosteric Inhibition of Androgen Receptors by Binding Function 3 Antagonists from an Integrated Molecular Modeling Study. J Chem Inf Model. 2021, 61(7):3477-94
Farago B, Nicholl ID, Wang S, Cheng X*, Callaway DJE*, Bu Z*. Activated nanoscale actin-binding domain motion in the catenin–cadherin complex revealed by neutron spin echo spectroscopy. Proc Natl Acad Sci USA. 2021, 118(13), e2025012118
Li J, Hu X, Neusius T, Cheng X, Smith MD, Godec A, Hong L, Metzler R, Smith JC. Reply to: Insufficient evidence for ageing in protein dynamics. Nat Phys. 2021, 17(7):775-6
Li T, Kong L, Li X, Wu S, Attri KS, Li Y, Gong W, Zhao B, Li L, Herring LE, Asara JM, Xu L, Luo X, Lei YL, Ma Q, Seveau S, Gunn JS, Cheng X, Singh PK, Green DR, Wang H, Wen H. Listeria monocytogenes upregulates mitochondrial calcium signalling to inhibit LC3-associated phagocytosis as a survival strategy. Nat Microbiol. 2021, 6(3):366-379
Persaud AK, Nair S, Rahman MF, Raj R, Weadick B, Nayak D, McElroy C, Shanmugam M, Knoblaugh S, Cheng X, Govindarajan R. Facilitative lysosomal transport of bile acids alleviates ER stress in mouse hematopoietic precursors. Nat Commun. 2021, 12(1):1248
Saeed AFUH, Chan C, Guan H, Gong B, Guo P*, Cheng X*, Ouyang S*. Structural Insights into gp16 ATPase in the Bacteriophage ϕ29 DNA Packaging Motor. Biochemistry. 2021, 60, 11, 886
Chan C, Du S, Dong Y*, X Cheng*. Computational and Experimental Approaches to Investigate Lipid Nanoparticles as Drug and Gene Delivery Systems. Curr Top Med Chem. 2021, 21(2), 92-114
Wu S, Chan C, Zhuang T, Li PK, Cheng X*. A computational study of effects on membrane recruitment of the polar linkers in Vitamin E derivatives. Biochim Biophys Acta (BBA)-General Subjects. 2020, 1864(10), 129655
Mostofian B, Johnson QR, Smith JC, Cheng X*. Carotenoids promote lateral packing and condensation of lipid membranes. Phys Chem Chem Phys. 2020, 22(21), 12281-93
Li W, Chan C, Zeng C, Turk R, Behlke MA, Cheng X*, Dong Y*. Rational Design of Small Molecules to Enhance Genome Editing Efficiency by Selectively Targeting Distinct Functional States of CRISPR-Cas12a. Bioconjugate Chem. 2020, 31(3):542-6
NT Cockroft, X Cheng*, JR Fuchs*. STarFish: A Stacked Ensemble Target Fishing Approach and its Application to Natural Products. J Chem Inf Model, 2019, 59 (11), 4906-4920
Cheng X*, Smith JC*. Biological Membrane Organization and Cellular Signaling. Chem Rev, 2019, 119, 95849-5880
Mostofian B, Zhuang T, Cheng X*, Nickels JD*. Branched-Chain Fatty Acid Content Modulates Structure, Fluidity and Phase in Model Microbial Cell Membranes. J Phys Chem B, 2019, 123, 5814−5821
Shrestha UR, Juneja P, Zhang Q, Gurumoorthy V, Borreguero JM, Urban V, Cheng X, Pingali SV, Smith JC, O’Neill HM, Petridis L. Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation. Proc Natl Acad Sci USA. 2019, 116(41):20446-20452
Guo P*, Driver D, Zhao Z, Zheng Z, Chan C, Cheng X. Controlling the Revolving and Rotating Motion Direction of Asymmetric Hexameric Nanomotor by Arginine Finger and Channel Chirality. ACS nano, 2019, 13(6):6207-23
Li Z, Zhang Y, Chan C, Zhi C, Cheng X*, Fan J*. Temperature-Dependent Lipid Extraction from Membranes by Boron Nitride Nanosheets. ACS nano, 2018, 12(3):2764-72
Ishita K, Stefanopoulos S, Khalil A, Cheng X, Tjarks W, Rappleye C. Synthesis and biological evaluation of aminothiazoles against Histoplasma capsulatum and Cryptococcus neoformans. Bioorg Med Chem, 2018, 26(9), 2251-2261
Johnson Q, Mostofian B, Gomez GF, Smith JC, Cheng X. Effects of Carotenoids on Lipid Bilayers. Phys Chem Chem Phys, 2018, 20, 3795-3804
Nickels JD*, Chatterjee S, Mostofian B, Stanley CB, Ohl M, Zolnierczuk P, Schulz R, Myles DAA, Standaert RF, Elkins JG, Cheng X*, Katsaras J. Bacillus subtilis Lipid Extract, A Branched-Chain Fatty Acid Model Membrane. J Phys Chem Lett. 2017, 4214-4217
Nickels JD, Chatterjee S, Stanley CB, Qian S, Cheng X, Myles DAA, Standaert RF, Elkins JG, Katsaras J. The in vivo structure of biological membranes and evidence for lipid domains. PLoS Biol. 2017, 15(5):e2002214
Hong L, Jain N, Cheng X, Bernal A, Tyagi M, Smith JC. Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering. Sci Adv. 2016, 2(10):e1600886
Tian J, Nickels J, Katsaras J, Cheng X*. Behavior of Bilayer Leaflets in Asymmetric Model Membranes: Atomistic Simulation Studies. J Phys Chem B. 2016, 120(33):8438-48
Hu X, Hong L, Smith MD, Neusius T, Cheng X, Smith JC. The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time. Nature Phys. 2016, 12, 171-174
Wu D, Fajer MI, Cao L, Cheng X, Yang W. Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways. Methods Enzymol. 2016;577:57-74
Nickels JD, Cheng X, Mostofian B, Stanley C, Lindner B, Heberle FA, Perticaroli S, Feygenson M, Egami T, Standaert RF, Smith JC, Myles DA, Ohl M, Katsaras J. Mechanical Properties of Nanoscopic Lipid Domains. J Am Chem Soc. 2015, 137(50):15772-80
Nickels JD, Smith JC, Cheng X*. Lateral organization, bilayer asymmetry, and inter-leaflet coupling of biological membranes. Chem Phys Lipids. 2015, 192:87-99
Chen Q, Luan ZJ, Cheng X*, Xu JH*. Molecular dynamics investigation of the substrate binding mechanism in carboxylesterase. Biochemistry. 2015, 54(9):1841-8
