My Bibliography

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Su M, Wang J, Xiang G, Do HN, Levitz J, Miao Y, Huang XY. Structural basis of agonist specificity of α(1A)-adrenergic receptor. Nat Commun. 2023 Aug 10;14(1):4819. doi: 10.1038/s41467-023-40524-2. PubMed PMID: 37563160; PubMed Central PMCID: PMC10415349.

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Do HN, Miao Y. Deep Boosted Molecular Dynamics: Accelerating Molecular Simulations with Gaussian Boost Potentials Generated Using Probabilistic Bayesian Deep Neural Network. J Phys Chem Lett. 2023 Jun 1;14(21):4970-4982. doi: 10.1021/acs.jpclett.3c00926. Epub 2023 May 23. PubMed PMID: 37219922; PubMed Central PMCID: PMC10355842.

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Vuckovic Z, Wang J, Pham V, Mobbs JI, Belousoff MJ, Bhattarai A, Burger WAC, Thompson G, Yeasmin M, Nawaratne V, Leach K, van der Westhuizen ET, Khajehali E, Liang YL, Glukhova A, Wootten D, Lindsley CW, Tobin A, Sexton P, Danev R, Valant C, Miao Y, Christopoulos A, Thal DM. Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics. Elife. 2023 May 30;12. doi: 10.7554/eLife.83477. PubMed PMID: 37248726; PubMed Central PMCID: PMC10229135.

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Pawnikar S, Bhattarai A, Ouyang SX, Vega R, Chen Y, Miao Y. Critical Non-Covalent Binding Intermediate for an Allosteric Covalent Inhibitor of SUMO E1. J Phys Chem Lett. 2023 Mar 23;14(11):2792-2799. doi: 10.1021/acs.jpclett.3c00253. Epub 2023 Mar 10. PubMed PMID: 36898086; PubMed Central PMCID: PMC10373441.

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Wang J, Miao Y. Ligand Gaussian Accelerated Molecular Dynamics 2 (LiGaMD2): Improved Calculations of Ligand Binding Thermodynamics and Kinetics with Closed Protein Pocket. J Chem Theory Comput. 2023 Feb 14;19(3):733-745. doi: 10.1021/acs.jctc.2c01194. Epub 2023 Jan 27. PubMed PMID: 36706316; PubMed Central PMCID: PMC10316156.

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Do HN, Devkota S, Bhattarai A, Wolfe MS, Miao Y. Effects of presenilin-1 familial Alzheimer's disease mutations on γ-secretase activation for cleavage of amyloid precursor protein. Commun Biol. 2023 Feb 14;6(1):174. doi: 10.1038/s42003-023-04539-1. PubMed PMID: 36788318; PubMed Central PMCID: PMC9929099.

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Wu X, Ramesh R, Wang J, Zheng Y, Armaly AM, Wei L, Xing M, Roy S, Lan L, Gao FP, Miao Y, Xu L, Aubé J. Small Molecules Targeting the RNA-Binding Protein HuR Inhibit Tumor Growth in Xenografts. J Med Chem. 2023 Feb 9;66(3):2032-2053. doi: 10.1021/acs.jmedchem.2c01723. Epub 2023 Jan 23. PubMed PMID: 36690437; PubMed Central PMCID: PMC10101218.

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Wang J, Bhattarai A, Do HN, Miao Y. Challenges and frontiers of computational modelling of biomolecular recognition. QRB Discov. 2022;3. doi: 10.1017/qrd.2022.11. Epub 2022 Aug 19. PubMed PMID: 37377636; PubMed Central PMCID: PMC10299731.

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Copeland MM, Do HN, Votapka L, Joshi K, Wang J, Amaro RE, Miao Y. Gaussian Accelerated Molecular Dynamics in OpenMM. J Phys Chem B. 2022 Aug 11;126(31):5810-5820. doi: 10.1021/acs.jpcb.2c03765. Epub 2022 Jul 27. PubMed PMID: 35895977; PubMed Central PMCID: PMC9773147.

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Su M, Paknejad N, Zhu L, Wang J, Do HN, Miao Y, Liu W, Hite RK, Huang XY. Structures of β(1)-adrenergic receptor in complex with Gs and ligands of different efficacies. Nat Commun. 2022 Jul 14;13(1):4095. doi: 10.1038/s41467-022-31823-1. PubMed PMID: 35835792; PubMed Central PMCID: PMC9283524.

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Wolfe MS, Miao Y. Structure and mechanism of the γ-secretase intramembrane protease complex. Curr Opin Struct Biol. 2022 Jun;74:102373. doi: 10.1016/j.sbi.2022.102373. Epub 2022 Apr 20. Review. PubMed PMID: 35461161; PubMed Central PMCID: PMC9189058.

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Bhattarai A, Devkota S, Do HN, Wang J, Bhattarai S, Wolfe MS, Miao Y. Correction to "Mechanism of Tripeptide Trimming of Amyloid β-Peptide 49 by γ-Secretase". J Am Chem Soc. 2022 May 25;144(20):9182. doi: 10.1021/jacs.2c04434. Epub 2022 May 11. PubMed PMID: 35544328; PubMed Central PMCID: PMC9809471.

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Pawnikar S, Magenheimer BS, Munoz EN, Maser RL, Miao Y. Mechanism of tethered agonist-mediated signaling by polycystin-1. Proc Natl Acad Sci U S A. 2022 May 10;119(19):e2113786119. doi: 10.1073/pnas.2113786119. Epub 2022 May 6. PubMed PMID: 35522707; PubMed Central PMCID: PMC9171645.

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Bhattarai A, Devkota S, Do HN, Wang J, Bhattarai S, Wolfe MS, Miao Y. Mechanism of Tripeptide Trimming of Amyloid β-Peptide 49 by γ-Secretase. J Am Chem Soc. 2022 Apr 13;144(14):6215-6226. doi: 10.1021/jacs.1c10533. Epub 2022 Apr 4. PubMed PMID: 35377629; PubMed Central PMCID: PMC9798850.

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Wang J, Bhattarai A, Do HN, Akhter S, Miao Y. Molecular Simulations and Drug Discovery of Adenosine Receptors. Molecules. 2022 Mar 22;27(7). doi: 10.3390/molecules27072054. Review. PubMed PMID: 35408454; PubMed Central PMCID: PMC9000248.

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Pawnikar S, Miao Y. Mechanism of Peptide Agonist Binding in CXCR4 Chemokine Receptor. Front Mol Biosci. 2022;9:821055. doi: 10.3389/fmolb.2022.821055. eCollection 2022. PubMed PMID: 35359589; PubMed Central PMCID: PMC8963245.

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Do HN, Wang J, Bhattarai A, Miao Y. GLOW: A Workflow Integrating Gaussian-Accelerated Molecular Dynamics and Deep Learning for Free Energy Profiling. J Chem Theory Comput. 2022 Mar 8;18(3):1423-1436. doi: 10.1021/acs.jctc.1c01055. Epub 2022 Feb 24. PubMed PMID: 35200019; PubMed Central PMCID: PMC9773012.

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Wang J, Miao Y. Protein-Protein Interaction-Gaussian Accelerated Molecular Dynamics (PPI-GaMD): Characterization of Protein Binding Thermodynamics and Kinetics. J Chem Theory Comput. 2022 Mar 8;18(3):1275-1285. doi: 10.1021/acs.jctc.1c00974. Epub 2022 Jan 31. PubMed PMID: 35099970; PubMed Central PMCID: PMC9817007.

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Célerse F, Inizan TJ, Lagardère L, Adjoua O, Monmarché P, Miao Y, Derat E, Piquemal JP. An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems. J Chem Theory Comput. 2022 Feb 8;18(2):968-977. doi: 10.1021/acs.jctc.1c01024. Epub 2022 Jan 26. PubMed PMID: 35080892.

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Do HN, Haldane A, Levy RM, Miao Y. Unique features of different classes of G-protein-coupled receptors revealed from sequence coevolutionary and structural analysis. Proteins. 2022 Feb;90(2):601-614. doi: 10.1002/prot.26256. Epub 2021 Oct 9. PubMed PMID: 34599827; PubMed Central PMCID: PMC8738117.

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Pawnikar S, Bhattarai A, Wang J, Miao Y. Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives. Adv Appl Bioinform Chem. 2022;15:1-19. doi: 10.2147/AABC.S247950. eCollection 2022. Review. PubMed PMID: 35023931; PubMed Central PMCID: PMC8747661.

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Wang J, Lan L, Wu X, Xu L, Miao Y. Mechanism of RNA recognition by a Musashi RNA-binding protein. Curr Res Struct Biol. 2022;4:10-20. doi: 10.1016/j.crstbi.2021.12.002. eCollection 2022. Review. PubMed PMID: 34988468; PubMed Central PMCID: PMC8695263.

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Höring C, Conrad M, Söldner CA, Wang J, Sticht H, Strasser A, Miao Y. Specific Engineered G Protein Coupling to Histamine Receptors Revealed from Cellular Assay Experiments and Accelerated Molecular Dynamics Simulations. Int J Mol Sci. 2021 Sep 17;22(18). doi: 10.3390/ijms221810047. PubMed PMID: 34576210; PubMed Central PMCID: PMC8467750.

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Draper-Joyce CJ, Bhola R, Wang J, Bhattarai A, Nguyen ATN, Cowie-Kent I, O'Sullivan K, Chia LY, Venugopal H, Valant C, Thal DM, Wootten D, Panel N, Carlsson J, Christie MJ, White PJ, Scammells P, May LT, Sexton PM, Danev R, Miao Y, Glukhova A, Imlach WL, Christopoulos A. Positive allosteric mechanisms of adenosine A(1) receptor-mediated analgesia. Nature. 2021 Sep;597(7877):571-576. doi: 10.1038/s41586-021-03897-2. Epub 2021 Sep 8. PubMed PMID: 34497422; PubMed Central PMCID: PMC8711093.

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Wang J, Arantes PR, Bhattarai A, Hsu RV, Pawnikar S, Huang YM, Palermo G, Miao Y. Gaussian accelerated molecular dynamics (GaMD): principles and applications. Wiley Interdiscip Rev Comput Mol Sci. 2021 Sep-Oct;11(5). doi: 10.1002/wcms.1521. Epub 2021 Mar 1. PubMed PMID: 34899998; PubMed Central PMCID: PMC8658739.

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Tang Z, Akhter S, Ramprasad A, Wang X, Reibarkh M, Wang J, Aryal S, Thota SS, Zhao J, Douglas JT, Gao P, Holmstrom ED, Miao Y, Wang J. Recognition of single-stranded nucleic acids by small-molecule splicing modulators. Nucleic Acids Res. 2021 Aug 20;49(14):7870-7883. doi: 10.1093/nar/gkab602. PubMed PMID: 34283224; PubMed Central PMCID: PMC8373063.

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Bhattarai A, Pawnikar S, Miao Y. Mechanism of Ligand Recognition by Human ACE2 Receptor. J Phys Chem Lett. 2021 May 27;12(20):4814-4822. doi: 10.1021/acs.jpclett.1c01064. Epub 2021 May 17. PubMed PMID: 33999630; PubMed Central PMCID: PMC8146134.

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Do HN, Akhter S, Miao Y. Pathways and Mechanism of Caffeine Binding to Human Adenosine A(2A) Receptor. Front Mol Biosci. 2021;8:673170. doi: 10.3389/fmolb.2021.673170. eCollection 2021. PubMed PMID: 33987207; PubMed Central PMCID: PMC8111288.

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Gao Y, Cao D, Pawnikar S, Akhter S, Miao Y, Liang B. Efficient purification and assembly of ribonucleoprotein complex for interaction analysis by MST assay coupled with GaMD simulations. STAR Protoc. 2021 Mar 19;2(1):100315. doi: 10.1016/j.xpro.2021.100315. eCollection 2021 Mar 19. PubMed PMID: 33659898; PubMed Central PMCID: PMC7890042.

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Wang J, Miao Y. Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding. J Chem Phys. 2020 Oct 21;153(15):154109. doi: 10.1063/5.0021399. PubMed PMID: 33092378; PubMed Central PMCID: PMC7575327.

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Conrad M, Söldner CA, Miao Y, Sticht H. Agonist Binding and G Protein Coupling in Histamine H(2) Receptor: A Molecular Dynamics Study. Int J Mol Sci. 2020 Sep 12;21(18). doi: 10.3390/ijms21186693. PubMed PMID: 32932742; PubMed Central PMCID: PMC7554837.

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Miao Y, Bhattarai A, Wang J. Ligand Gaussian Accelerated Molecular Dynamics (LiGaMD): Characterization of Ligand Binding Thermodynamics and Kinetics. J Chem Theory Comput. 2020 Sep 8;16(9):5526-5547. doi: 10.1021/acs.jctc.0c00395. Epub 2020 Aug 7. PubMed PMID: 32692556; PubMed Central PMCID: PMC7768792.

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Gao Y, Cao D, Pawnikar S, John KP, Ahn HM, Hill S, Ha JM, Parikh P, Ogilvie C, Swain A, Yang A, Bell A, Salazar A, Miao Y, Liang B. Structure of the Human Respiratory Syncytial Virus M2-1 Protein in Complex with a Short Positive-Sense Gene-End RNA. Structure. 2020 Sep 1;28(9):979-990.e4. doi: 10.1016/j.str.2020.07.001. Epub 2020 Jul 21. PubMed PMID: 32697936; PubMed Central PMCID: PMC7484405.

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Lan L, Liu J, Xing M, Smith AR, Wang J, Wu X, Appelman C, Li K, Roy A, Gowthaman R, Karanicolas J, Somoza AD, Wang CCC, Miao Y, De Guzman R, Oakley BR, Neufeld KL, Xu L. Identification and Validation of an Aspergillus nidulans Secondary Metabolite Derivative as an Inhibitor of the Musashi-RNA Interaction. Cancers (Basel). 2020 Aug 8;12(8). doi: 10.3390/cancers12082221. PubMed PMID: 32784494; PubMed Central PMCID: PMC7463734.

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Bhattarai A, Wang J, Miao Y. Retrospective ensemble docking of allosteric modulators in an adenosine G-protein-coupled receptor. Biochim Biophys Acta Gen Subj. 2020 Aug;1864(8):129615. doi: 10.1016/j.bbagen.2020.129615. Epub 2020 Apr 13. PubMed PMID: 32298791; PubMed Central PMCID: PMC7261249.

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Pawnikar S, Miao Y. Pathway and mechanism of drug binding to chemokine receptors revealed by accelerated molecular simulations. Future Med Chem. 2020 Jul;12(13):1213-1225. doi: 10.4155/fmc-2020-0044. Epub 2020 Jun 9. PubMed PMID: 32515227; PubMed Central PMCID: PMC7367101.

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Bhattarai A, Devkota S, Bhattarai S, Wolfe MS, Miao Y. Mechanisms of γ-Secretase Activation and Substrate Processing. ACS Cent Sci. 2020 Jun 24;6(6):969-983. doi: 10.1021/acscentsci.0c00296. Epub 2020 Jun 4. PubMed PMID: 32607444; PubMed Central PMCID: PMC7318072.

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Bhattarai A, Wang J, Miao Y. G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation State. J Comput Chem. 2020 Feb 15;41(5):460-471. doi: 10.1002/jcc.26082. Epub 2019 Oct 10. PubMed PMID: 31602675; PubMed Central PMCID: PMC7026935.

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Wang J, Bhattarai A, Ahmad W, Farnan T, John K, Miao Y. Computer-aided GPCR drug discovery. In: Jastrzebska B, Park P, editors. GPCRs: Structure, Function, and Drug Discovery [Internet] Cleveland, OH, USA: Academic Press; 2020. Chapter 15; p.283-293. 283-293p. Available from: http://www.sciencedirect.com/science/article/pii/B9780128162286000155.

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Wang J, Alekseenko A, Kozakov D, Miao Y. Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations. Front Mol Biosci. 2019;6:112. doi: 10.3389/fmolb.2019.00112. eCollection 2019. PubMed PMID: 31737642; PubMed Central PMCID: PMC6835073.

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Wang J, Miao Y. Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors. J Phys Chem B. 2019 Aug 1;123(30):6462-6473. doi: 10.1021/acs.jpcb.9b04867. Epub 2019 Jul 22. PubMed PMID: 31283874; PubMed Central PMCID: PMC7026936.

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Ricci CG, Chen JS, Miao Y, Jinek M, Doudna JA, McCammon JA, Palermo G. Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics. ACS Cent Sci. 2019 Apr 24;5(4):651-662. doi: 10.1021/acscentsci.9b00020. Epub 2019 Mar 7. PubMed PMID: 31041385; PubMed Central PMCID: PMC6487449.

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Huang YM, Munguia J, Miao Y, Nizet V, McCammon JA. Docking simulation and antibiotic discovery targeting the MlaC protein in Gram-negative bacteria. Chem Biol Drug Des. 2019 Apr;93(4):647-652. doi: 10.1111/cbdd.13462. Epub 2019 Feb 19. PubMed PMID: 30570806; PubMed Central PMCID: PMC6737922.

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Wang J, Miao Y. Recent advances in computational studies of GPCR-G protein interactions. Adv Protein Chem Struct Biol. 2019;116:397-419. doi: 10.1016/bs.apcsb.2018.11.011. Epub 2019 Jan 3. Review. PubMed PMID: 31036298; PubMed Central PMCID: PMC6986689.

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Miao Y, Bhattarai A, Nguyen ATN, Christopoulos A, May LT. Structural Basis for Binding of Allosteric Drug Leads in the Adenosine A(1) Receptor. Sci Rep. 2018 Nov 15;8(1):16836. doi: 10.1038/s41598-018-35266-x. PubMed PMID: 30442899; PubMed Central PMCID: PMC6237911.

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Bhattarai A, Miao Y. Gaussian accelerated molecular dynamics for elucidation of drug pathways. Expert Opin Drug Discov. 2018 Nov;13(11):1055-1065. doi: 10.1080/17460441.2018.1538207. Epub 2018 Oct 29. Review. PubMed PMID: 30371112; PubMed Central PMCID: PMC6450802.

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Zhang J, Wang N, Miao Y, Hauser F, McCammon JA, Rappel WJ, Schroeder JI. Identification of SLAC1 anion channel residues required for CO(2)/bicarbonate sensing and regulation of stomatal movements. Proc Natl Acad Sci U S A. 2018 Oct 30;115(44):11129-11137. doi: 10.1073/pnas.1807624115. Epub 2018 Oct 9. PubMed PMID: 30301791; PubMed Central PMCID: PMC6217375.

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Utesch T, de Miguel Catalina A, Schattenberg C, Paege N, Schmieder P, Krause E, Miao Y, McCammon JA, Meyer V, Jung S, Mroginski MA. A Computational Modeling Approach Predicts Interaction of the Antifungal Protein AFP from Aspergillus giganteus with Fungal Membranes via Its γ-Core Motif. mSphere. 2018 Oct 3;3(5). doi: 10.1128/mSphere.00377-18. PubMed PMID: 30282755; PubMed Central PMCID: PMC6170789.

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Miao Y. Acceleration of biomolecular kinetics in Gaussian accelerated molecular dynamics. J Chem Phys. 2018 Aug 21;149(7):072308. doi: 10.1063/1.5024217. PubMed PMID: 30134710; PubMed Central PMCID: PMC6901173.

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Amaro RE, Baudry J, Chodera J, Demir Ö, McCammon JA, Miao Y, Smith JC. Ensemble Docking in Drug Discovery. Biophys J. 2018 May 22;114(10):2271-2278. doi: 10.1016/j.bpj.2018.02.038. Epub 2018 Mar 30. Review. PubMed PMID: 29606412; PubMed Central PMCID: PMC6129458.