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Department of Pharmacology

Publications

Google Scholar

*(Co)-corresponding author, #Equal contributions, Undergraduate

Preprints/In Review

  1. Lou J-S, Su M, Wang J, Do HN, Miao Y, & Huang X-Y (2024) Distinct Epinephrine Conformations Binding to α- and β-Adrenergic Receptors. Experimental & Molecular Medicine. In Review.

Reviews and Book Chapters

  1. Miao Y* & Wolfe MS* (2024) Emerging Structures and Dynamic Mechanisms of Gamma-Secretase. Neural Regeneration Research, Published Online. https://doi.org/10.4103/NRR.NRR-D-23-01781 (Abstract | PDF)
  2. Koirala K, Joshi K, Adediwura V, Wang J, Do H, & Miao Y* (2024) Accelerating molecular dynamics simulations for drug discovery. Computational Drug Discovery and Design, Second Edition, Edited by Mohini Gore and Umesh B. Jagtap, Methods in Molecular Biology. 2714:187-202. (Abstract | PDF)
  3. Do HN, Wang J, Joshi K, Koirala K, & Miao Y* (2023) Chapter 2 – Gaussian accelerated Molecular Dynamics in Drug Discovery. Computational Drug Discovery Methods and Applications, Edited by Poongavanam V & Ramaswamy V (Wiley). 1: 21-43. (Abstract | PDF)
  4. Pawnikar S, Akhter S, & Miao Y* (2023) Structural dynamics of chemokine receptors. Vitamins and Hormones, Edited by Dr. Gerald Litwack G, Vitamins and Hormones, 123: 645-662. (Abstract | PDF)
  5. Wang J, Do HN, Koirala K & Miao Y* (2022) Predicting biomolecular binding kinetics: A review. Journal of Chemical Theory and Computation, Cover Highlight, 19(8):2135-2148. (Abstract | PDF)
  6. Wang J, Bhattarai A, Do HN, & Miao Y* (2022) Challenges and Frontiers of Computational Modeling of Biomolecular Recognition. QRB Discovery, 3, E13.   (Abstract | PDF)
  7. Wolfe MS & Miao Y (2022) Structure and mechanism of the γ-Secretase intramembrane protease complex. Curr Opin Struct Biol, 74:102373.  (Abstract | PDF)
  8. Wang J, Bhattarai A, Do H, Akhter S, & Miao Y* (2022) Molecular simulations and drug discovery of adenosine receptors. Molecules, 27(7):2054. (Abstract | PDF)
  9. Pawnikar S, Bhattarai A, Wang J and Miao Y.* (2022) Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives. Adv Appl Bioinform Chem, 15:1-19. (Abstract | PDF)
  10. Wang J, Arantes P, Bhattarai A, Hsu R, Pawnikar S, Huang Y-M, Palermo G* and Miao Y* (2021) Gaussian accelerated molecular dynamics: principles and applications. WIREs Computational Molecular Science: e1521. (Abstract | PDF)
    • Advanced Science News: A “time-accelerated computational microscope” provides biologists with powerful insights
  11. Wang, J.; Bhattarai, A.; Ahmad, W. I.; Farnan, T. S.; John, K. P.; Miao, Y., Computer-Aided GPCR Drug Discovery, Elsevier book “GPCRs: Structure, Function, and Drug Discovery”, Edited by Dr. Paul Shin-Hyun Park and Dr. Beata Jastrzebska, 283-293. (Abstract | PDF)
  12. Wang, J., and Miao, Y.* (2019) Recent advances in computational studies of GPCR-G protein interactions, Advances in Protein Chemistry and Structural Biology, 116, 397-419. (Abstract | PDF)

Research Articles

  1. Pawnikar S, Magenheimer BS, Munoz EN, Haldane A, Maser RL*, & Miao Y* (2024) Activation of Polycystin-1 Signaling by Binding of Stalk-derived Peptide Agonists. eLife Preprint, 13:RP95992. https://doi.org/10.7554/eLife.95992.1
  2. Devkota S, Zhou R, Nagarajan V, Maesako M, Do H, Noorani A, Overmeyer C, Bhattarai S, Douglas JT, Saraf A, Miao Y, Ackley BD, Shi Y, & Wolfe MS (2024) Familial Alzheimer mutations stabilize synaptotoxic gamma-secretase-substrate complexes. Cell Rep, 43(2):113761.
  3. Adediwura VA & Miao Y* (2024) Mechanistic Insights into Peptide Binding and Deactivation of an Adhesion G Protein-Coupled Receptor. Molecules. 29(1):164.
  4. Akhter S, Tang Z, Wang J, Haboro M, Holmstrom ED, Wang J, & Miao Y* (2024) Mechanism of ligand binding to theophylline RNA aptamer. Journal of Chemical Information and Modeling, 64(3):1017-1029.
  5. Do HN#, Malvankar SR#, Wolfe MS*, & Miao Y* (2023) Molecular dynamics activation of gamma-secretase for cleavage of Notch1 substrate. ACS Chemical Neurosciences, 14(23):4216-4226. (Abstract | PDF) 
  6. Do HN, Wang J, & Miao Y* (2023) Deep learning dynamic allostery of G-protein-coupled receptors. JACS Au, 3 (11): 3165–3180. (Abstract | PDF) 
  7. Su, M.#, Wang, J.#, Xiang, G., Do, H.N., Levitz, J., Miao, Y.*, Huang, X.-Y.* (2023) Structural Basis of Agonist Specificity of alpha(1A)-Adrenergic Receptor. Nature Communications. 14: 4819.  (Abstract | PDF)
  8. Do HN & Miao Y* (2023) Deep Boosted Molecular Dynamics (DBMD): Accelerating molecular simulations with Gaussian boost potentials generated using probabilistic Bayesian deep neural network. Journal of Physical Chemistry Letters, 14 (21): 4970-4982.  (Abstract | PDF)
  9. Vuckovic Z#, Wang J#, Pham V#, Mobbs J#, Belousoff MJ, Bhattarai A, Nawaratne V, Leach K, Burger WAC, Westhuizen ETvd, Khajehali E, Thompson G, Yeasmin M, Liang Y-L, Glukhova A, Wootten D, Lindsley CW, Tobin AB, Sexton PM, Danev R, Valant C, Miao Y*, Christopoulos A*, & Thal DM* (2022) Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics. eLife, 12:e83477.  (Abstract | PDF)
  10. Pawnikar S, Bhattarai A, Ouyang SX, Vega R, Chen Y*, & Miao Y* (2023) Critical Non-Covalent Binding Intermediate for an Allosteric Covalent Inhibitor of SUMO E1. J Phys Chem Lett, 14(11):2792-2799.  (Abstract | PDF)
  11. Do HN#, Devkota S#, Bhattarai A, Wolfe MS*, & Miao Y* (2022) Effects of Presenilin-1 Familial Alzheimer’s Disease Mutations on γ-Secretase Activation for Cleavage of Amyloid Precursor Protein. Communications Biology, 6(1):174.  (Abstract | PDF)
  12. Wu X, Ramesh R, Wang J, Zheng Y, Armaly AM, Wei L, Xing M, Roy S, Lan L, Gao FP, Miao Y, Xu L, & Aube J (2023) Small Molecules Targeting the RNA-Binding Protein HuR Inhibit Tumor Growth in Xenografts. J Med Chem, 66(3):2032-2053.  (Abstract | PDF)
  13. Wang J & Miao Y* (2022) Ligand Gaussian accelerated molecular dynamics 2 (LiGaMD2): Improved calculations of ligand binding thermodynamics and kinetics with closed protein pocket. Journal of Chemical Theory and Computation, 19(3): 733–745.  (Abstract | PDF)
  14. Copeland M#, Do HN#, Votapka L, Joshi K, Wang J, Amaro RE, & Miao Y* (2022) Gaussian accelerated molecular dynamics in OpenMM. Journal of Physical Chemistry B, 126(31): 5810–5820.  (Abstract | PDF)
  15. Su M, Paknejad N, Zhu L, Wang J, Do HN, Miao Y, Liu W, Hite RK, & Huang X-Y (2022) Structures of β1-adrenergic receptor in complex with Gs and ligands of different efficacies. Nature Communications, 13: 4095.  (Abstract | PDF)
  16. Pawnikar, S., Magenheimer, B.S., Nevarez-Munoz, E., Maser, R.L.*, and Miao, Y.* (2022). Mechanism of Tethered Agonist-Mediated Signaling by Polycystin-1. Proc Natl Acad Sci U S A, 119(19):e2113786119.  (Abstract | PDF)
  17. Bhattarai, A., Devkota, S., Do, H.N., Wang, J., Bhattarai, S., Wolfe, M.S.*, and Miao, Y.* (2022). Mechanism of Tripeptide Trimming of Amyloid β-Peptide 49 by γ-Secretase. Journal of American Chemical Society, 144(14): 6215-6226.  (Abstract | PDF)
  18. Pawnikar S & Miao Y* (2022) Mechanism of Peptide Agonist Binding in CXCR4 Chemokine Receptor. Frontiers in Molecular Biosciences, 9:821055.  (Abstract | PDF)
  19. Do HN, Wang J, Bhattarai A, & Miao Y* (2022) GLOW: A workflow integrating Gaussian accelerated molecular dynamics and Deep Learning for free energy profiling. Journal of Chemical Theory and Computation, 18(3):1423-1436. (Abstract | PDF)
  20. Célerse F, Inizan TJ, Lagardère L, Adjoua O, Monmarché P, Miao Y, Derat E, & Piquemal J-P (2022) An Efficient Gaussian-Accelerated Molecular Dynamics (GaMD) Multilevel Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems. Journal of Chemical Theory and Computation, 18(2):968-977. (Abstract | PDF)
  21. Wang, J. and Miao, Y*, (2022) Protein-protein interaction-Gaussian accelerated molecular dynamics (PPI-GaMD): Characterization of protein binding thermodynamics and kinetics. Journal of Chemical Theory and Computation, 18(3):1275-1285.  (Abstract | PDF)
  22. Wang J, Lan L, Wu X, Xu L, & Miao Y* (2022) Mechanism of RNA recognition by a Musashi RNA-binding protein. Current Research in Structural Biology, 4:10-20.  (Abstract | PDF)
  23. Do HN, Haldane A*, Levy RM, & Miao Y* (2021) Unique Features of Different Classes of G-Protein-Coupled Receptors Revealed from Sequence Coevolutionary and Structural Analysis. Proteins: Structure Function and Bioinformatics, 90(2):601-614.  (Abstract | PDF)
  24. Draper-Joyce CJ, Bhola R, Wang J, Bhattarai A, Nguyen ATN, Cowie-Kent I, O’Sullivan K, Venugopal H, Valant C, Thal DM, Wootten D, Panel N, Carlsson J, Christie MJ, Scammells P, May LT, Sexton PM, Danev R, Miao Y, Glukhova A, Wendy L I, Christopoulos A (2021) Positive allosteric mechanisms of adenosine A1 receptor-mediated analgesia. Nature, 597 (7877): 571-576. (Abstract | PDF)
  25. Tang Z, Akhter S, Ramprasad A, Wang X, Reibarkh M, Wang J, Aryal S, Thota S, Zhao J, Douglas J, Gao P, Holmstrom E, Miao Y*, & Wang J* (2021) Recognition of single-stranded nucleic acids by small-molecule splicing modulators. Nucleic Acids Research, 49(14):7870-7883.   (Abstract | PDF)
  26. Bhattarai A, Pawnikar S, & Miao Y* (2021) Mechanism of ligand recognition by human ACE2 receptor. J Phys Chem Lett, 12:4814-4822.  (Abstract | PDF)
  27. Do, H. N., Akhter, S. & Miao, Y.* (2021) Pathways and Mechanism of Caffeine Binding to Human Adenosine A2A Receptor. Frontiers in Molecular Biosciences 8, 242.  (Abstract | PDF)
  28. Gao, Y.; Cao, D.; Pawnikar, S.; Akhter, S.; Miao, Y.*; Liang, B.*, (2021) Efficient purification and assembly of ribonucleoprotein complex for interaction analysis by MST assay coupled with GaMD simulations. STAR Protocols, 2(1), 100315.  (Abstract | PDF)
  29. Conrad M, Soldner CA, Miao Y, & Sticht H (2020) Agonist Binding and G Protein Coupling in Histamine H2 Receptor: A Molecular Dynamics Study. International Journal of Molecular Sciences, 21(18):6693.  (Abstract | PDF)
  30. Wang, J. and Miao, Y*, (2020) Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding. Journal of Chemical Physics, 153, 154109. (Abstract | PDF)
  31. Miao, Y*, Bhattarai, A., and Wang, J. (2020) Ligand Gaussian accelerated molecular dynamics (LiGaMD): Characterization of ligand binding thermodynamics and kinetics. Journal of Chemical Theory and Computation, 16(9): 5526-5547. (Abstract | PDF)
  32. Gao, Y.; Cao, D.; Pawnikar, S.; John, K. P.; Ahn, H. M.; Hill, S.; Ha, J. M.; 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, 28(9):979-990.  (Abstract | PDF)
  33. Lan, L.; Liu, J.; Xing, M.; Smith, A.R.; Wang, J.; Wu, X.; Appelman, C.; Li, K.; Roy, A.; Gowthaman, R.; Karanicolas, J.; Somoza, A.D.; Wang, C.C.C.; Miao, Y.; De Guzman, R.; Oakley, B.R.; Neufeld, K.L.; Xu, L. (2020) Identification and Validation of an Aspergillus nidulans Secondary Metabolite Derivative as an Inhibitor of the Musashi-RNA Interaction. Cancers, 12, 2221. (Abstract | PDF)
  34. Bhattarai, A., Devkota, S., Bhattarai, S., Wolfe, M. S.* & Miao, Y.* (2020) Mechanisms of gamma-secretase activation and substrate processing. ACS Central Science, 6(6), 969-983. (Abstract | PDF)
  35. Pawnikar, S. and Miao, Y.* (2020) Pathway and Mechanism of Drug Binding to Chemokine Receptors Revealed by Accelerated Molecular Simulations, Future Medicinal Chemsitry, 12(13):1213-1225. (Abstract | PDF)
  36. Bhattarai, A.#, Wang, J.#, and Miao, Y.* (2020) Retrospective Ensemble Docking of Allosteric Modulators in an Adenosine G-Protein-Coupled Receptor, Special Issue “Advances in Computational Molecular Biophysics”, BBA – General Subjects, 6: 112. (Abstract | PDF) Free access until June 10, 2020.
  37. Wang, J., Alekseenko, A, Kozakov, D. and Miao, Y.* (2019) Improved Modeling of Peptide-Protein Binding through Global Docking and Accelerated Molecular Dynamics Simulations,  Special Issue “Multiscale Modeling from Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations”,  Frontiers in Molecular Biosciences, 6: 112. (Abstract | PDF)
  38. Bhattarai, A.#, Wang, J.#, and Miao, Y.* (2019) G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation state, J. Comp. Chem., Special Issue “Membrane Protein Simulations”, 41 (5), 460-471. (Abstract | PDF)
  39. Wang, J., and Miao, Y.* (2019) Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors, Journal of Physical Chemistry B, 123, 6462-6473. (Abstract | PDF)
    • Highlighted on the journal cover: “Specific G protein coupling to adenosine G-protein-coupled receptors revealed from all-atom enhanced sampling simulations: the adenosine A1 receptor (A1AR) prefers to bind the Gi protein to the Gs. The Gs could not stabilize adenosine binding in the active A1AR and vice versa. In contrast, the adenosine A2A receptor (A2AAR) could bind both the Gs and Gi proteins.”
  40. Ricci, C. G., Chen, J. S., Miao, Y., Jinek, M., Doudna, J. A., McCammon, J. A., and Palermo, G. (2019) Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics, ACS Central Science, 5(4): 651-662. (Abstract | PDF)
  41. Miao, Y.*, Bhattarai, A., Nguyen, A. T., Christopoulos, A., and May, L. T. (2018) Structural Basis for Binding of Allosteric Drug Leads in the Adenosine A1 Receptor, Scientific Reports, 8:16836. (Abstract | PDF)
  42. Bhattarai, A., and Miao, Y.* (2018) Gaussian Accelerated Molecular Dynamics for Elucidation of Drug Pathways, Expert Opinion On Drug Discovery.13(11):1055-1065. (Abstract | PDF)
  43. Huang YM, Munguia J, Miao Y, Nizet V, & McCammon JA (2018) Docking simulation and antibiotic discovery targeting the MlaC protein in Gram-negative bacteria. Chem Biol Drug Des., 93 (4), 647-652. (Abstract | PDF)
  44. Zhang, J., Wang, N., Miao, Y.*, Hauser, F., Rappel, W.-J., McCammon, J. A., and Schroeder, J.* (2018) Identification of SLAC1 anion channel residues required for CO2/bicarbonate sensing and regulation of stomatal movements, Proc Natl Acad Sci, 115 (44) 11129-11137. (Abstract | PDF)
  45. Utesch, T., Catalina, A. d. M., Schattenberg, C., Paege, N., Schmieder, P., Krause, E., Miao, Y., McCammon, J. A., Meyer, V., Jung, S., and Mroginski, M. (2018) A computational modelling approach predicts interaction of the antifungal protein AFP from Aspergillus giganteus with fungal membranes via its γ-core motif, mSphere, 3(5), e00377-18. (Abstract | PDF)
  46. Miao, Y. (2018). “Acceleration of Biomolecular Kinetics in Gaussian Accelerated Molecular Dynamics.” Journal of Chemical Physics, 149(7): 072308. (Abstract | PDF)
  47. Amaro, R. E., J. Baudry, J. Chodera, Ö. Demir, J. A. McCammon, Y. Miao and J. C. Smith (2018). “Ensemble Docking in Drug Discovery.” Biophysical Journal,114(10): 2271-78. (Abstract | PDF)
  48. Huang, Y. M.*, J. A. McCammon and Y. Miao* (2018). “Replica exchange Gaussian accelerated molecular dynamics: Improved enhanced sampling and free energy calculation.” J Chem Theory Comput, 14(4): 1853-64. (Abstract | PDF)
  49. Miao Y* & McCammon JA* (2018) Mechanism of the G-Protein Mimetic Nanobody Binding to a Muscarinic G-Protein-Coupled Receptor. Proc Natl Acad Sci U S A, 115(12): 3036-41. (Abstract | PDF)
    •Extreme Science and Engineering Discovery Environment (XSEDE) Science Stories: “XSEDE Helps Reveal How a Heart Drug Molecular Switch Is Turned On and Off”
    •San Diego Supercomputer News: “SDSC Simulations Reveal How a Heart Drug Molecular Switch Is Turned On and Off”
  50. Miao Y*, Huang YM*, Walker R, Chang C-eA, & McCammon JA (2018) Ligand Binding Pathways and Conformational Transitions of the HIV Protease. Biochemistry, 57(9): 1533-41. (Abstract | PDF)

Software

  1. Case, D. A., K. Belfon, I. Y. Ben-Shalom, S. R. Brozell, D. S. Cerutti, I. T.E. Cheatham, V. W. D. Cruzeiro, T. A. Darden, R. E. Duke, G. Giambasu, M. K. Gilson, H. Gohlke, A. W. Goetz, R. Harris, S. Izadi, K. K.-. jhala, A. Kovalenko, R. Krasny, T. Kurtzman, T. S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, V. Man, K. M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, A. Onufriev, F. Pan, S. Pantano, R. Qi, D. R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C. L. Simmerling, N. Skrynnikov, J. Smith, J. Swails, R. C. Walker, J. Wang, L. Wilson, R. M. Wolf, X. Wu, D. M. York and P. A. Kollman (2022). AMBER 22, University of California, San Francisco.
  2. Case, D. A., K. Belfon, I. Y. Ben-Shalom, S. R. Brozell, D. S. Cerutti, I. T.E. Cheatham, V. W. D. Cruzeiro, T. A. Darden, R. E. Duke, G. Giambasu, M. K. Gilson, H. Gohlke, A. W. Goetz, R. Harris, S. Izadi, K. K.-. jhala, A. Kovalenko, R. Krasny, T. Kurtzman, T. S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, V. Man, K. M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, A. Onufriev, F. Pan, S. Pantano, R. Qi, D. R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C. L. Simmerling, N. Skrynnikov, J. Smith, J. Swails, R. C. Walker, J. Wang, L. Wilson, R. M. Wolf, X. Wu, D. M. York and P. A. Kollman (2020). AMBER 20, University of California, San Francisco.
  3. Case, D. A., I. Y. Ben-Shalom, S. R. Brozell, D. S. Cerutti, I. T.E. Cheatham, V. W. D. Cruzeiro, T. A. Darden, R. E. Duke, D. Ghoreishi, M. K. Gilson, H. Gohlke, A. W. Goetz, D. Greene, R. Harris, N. Homeyer, S. Izadi, A. Kovalenko, T. Kurtzman, T. S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D. J. Mermelstein, K. M. Merz, Y. Miao, G. Monard, C. Nguyen, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D. R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C. L. Simmerling, J. Smith, R. Salomon-Ferrer, J. Swails, R. C. Walker, J. Wang, H. Wei, R. M. Wolf, X. Wu, L. Xiao, D. M. York and P. A. Kollman (2018). AMBER 18, University of California, San Francisco.

Editorials

  1. Miao Y*, Chang C-EA*, Zhu W*, & McCammon JA* (2023) Editorial: Mechanisms, thermodynamics and kinetics of ligand binding revealed from molecular simulations and machine learning. Frontiers in Molecular Biosciences, 10.

Prior to KU:

Research Articles

  1. G Palermo, Y Miao, RC Walker, M Jinek, JA McCammon (2017), CRISPR-Cas9 conformational activation elucidated through the computational microscope. Proc Natl Acad Sci U S A, 114(28), 7260-7265. (Abstract | PDF)
    • UCSD News, Science Daily: “Novel molecular dynamics captures atomic-level detail of CRISPR-Cas9 activity”
  2. Caliman, A., Miao, Y., McCammon, J.A. (2017), Mapping the allosteric sites of the A2a adenosine receptor. Chemical Biology & Drug Design, DOI: 10.1111/cbdd.13053. (Abstract | PDF)
  3. Caliman, A., Miao, Y., McCammon, J.A. (2017), Activation Mechanisms of the First Sphingosine-1-Phosphate Receptor. Protein Science, 26(6), 1150-1160. (Abstract | PDF)
  4. Pang, Y.T.#, Y. Miao#,*, Y. Wang* and J. A. McCammon* (2017) Gaussian accelerated molecular dynamics in NAMD, J Chemical Theory and Computation, 13(1): 9-19. (Abstract | PDF)
  5. Anderson, O. J., M. W. Risør, E. C. Poulsen, N. C. Nielsen, Y. Miao, J. J. Enghild and B. Schiøtt (2017), The reactive center loop insertion in a-1-antitrypsin captured by accelerated molecular dynamics simulation.Biochemistry, 56 (4): 634–646. (Abstract | PDF)
  6. Grouleff, J., H. Koldsø, Y. Miao and B. Schiøtt (2017), Ligand binding in the extracellular vestibule of the neurotransmitter transporter homologue LeuT.ACS Chemical Neuroscience, 8 (3): 619–628. (Abstract | PDF)
  7. Miao Y.* and McCammon, J. A. (2016) Graded activation and free energy landscapes of a muscarinic G protein-coupled receptor. Proc Natl Acad Sci U S A, 113(43): 12162–12167. (Abstract | PDF)
  8. Miao Y.*,#, Goldfeld D, Moo EV, Sexton PM, Christopoulos A, McCammon J. A.* and Valant C.*,# (2016) Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor. Proc Natl Acad Sci U S A 113(38): E5675–E5684. (Abstract | PDF)
    • UCSD News, Science Daily: “Promising Drug Leads Identified to Combat Heart Disease”
    • Health Medicinet: “Researchers use unique computational approach to identify promising drug leads for heart diseases”
  9. G Palermo, Y Miao, RC Walker, M Jinek, JA McCammon (2016) Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations, ACS Central Science, 2(10): 756-763. (Abstract | PDF)
    • UCSD News: “SDSC Supercomputer Modeling Reveals Acrobatics of CRISPR-Cas9 Technology”
  10. YM Huang, Y Miao, J Munguia, L Lin, V Nizet, JA McCammon (2016), Molecular dynamic study of MlaC protein in Gram-negative bacteria: conformational flexibility, solvent effect and protein-phospholipid binding, Protein Science, 25(8): 1430–1437. (Abstract | PDF)
  11. Huber, G., Y. Miao, S. Zhou, B. Li and J. A. McCammon (2016), Hybrid Finite Element and Brownian Dynamics Method for Charged Particles, J Chem Phys 144: 164107. (Abstract | PDF)
  12. Miao, Y.*, J. Baudry, J. C. Smith and McCammon JA (2015) General Trends of Dihedral Conformational Transitions in a Globular Protein. Proteins-Structure Function and Bioinformatics 84: 501-514. (Abstract | PDF)
  13. Miao, Y.*, Feher V. and McCammon JA (2015) Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation. J Chemical Theory and Computation, 11(8): 3584-3595. (Abstract | PDF)
    • Cover Highlight: J. Andrew McCammon Festschrift special issue, J. Phys. Chem. B (2016) “Benzene ligand binding to T4 lysozyme, and corresponding free energy surface. The newest MD method from the McCammon group is Gaussian Accelerated Molecular Dynamics (GaMD), developed primarily by Dr. Yinglong Miao (Miao, Y.; et al. J. Chem. Theory Comput. 2015, 11,3584–3595). The method draws upon remarkable advances in theory and computers since the first protein MD simulation (McCammon, J.A.; et al. Nature 1977, 267,585–590). That first simulation covered 9 ps for a 58-residue protein with four explicit solvent molecules. GaMD allows simulations of systems containing hundreds of thousands of atoms, sampling configurations that evolve on millisecond timescales; corresponding free energy landscapes can be calculated by careful reweighting …”
    • Lecture, NBCR-TCBG joint workshop “Simulation-Based Drug Discovery” (2015)
    • Invited Talk, Snowmass Free Energy Calculation Workshop (2015)
    • Invited Talk, 2016 American Chemical Society Meeting (2016)
    • Invited Talk,Vertex Workshop on Free Energy Methods in Drug Design: Targeting Cancer” (2016)
  14. Miao, Y.#,*, F. Feixas#,*, C. Eun#,*and J. A. McCammon (2015) Accelerated molecular dynamics simulations of protein folding. J. Comp. Chem., 36(20): 1536-1549. (Abstract | PDF)
  15. Kappel, K., Miao, Y.* and J. A. McCammon (2015). Accelerated Molecular Dynamics Simulations of Ligand Binding to a Muscarinic G-protein Coupled Receptor. Quarterly Reviews of Biophysics, DOI: 10.1017/S0033583515000153. (Abstract | PDF)
  16. Miao, Y.*, Caliman A, McCammon JA (2015) Allosteric Effects of Sodium Ion Binding on Activation of the M3 Muscarinic G-Protein-Coupled Receptor. Biophysical J., 108(7): 1796–1806. (Abstract | PDF)
  17. Caliman AD, Swift S, Wang Y, Miao, Y., McCammon JA (2015) Investigation of the conformational dynamics of the Apo A2A adenosine structure. Protein Science, 24(6): 1004-1012. (Abstract | PDF)
  18. Ellingson SR, Miao Y, Baudry J, Smith JC (2014) Multi-Conformer Ensemble Docking to Difficult Protein Targets. J. Phys. Chem. B, 119(3): 1026–1034. (Abstract | PDF)
  19. Miao Y*, Sinko W, Pierce L, Bucher D, Walker RC, McCammon JA (2014) Improved reweighting of accelerated molecular dynamics simulations for free energy calculation. J Chemical Theory and Computation, 10(7): 2677–2689. (Abstract | PDF)
  20. Miao Y*, Nichols SE*, McCammon JA (2014) Free energy landscapes of G-protein-coupled receptors, explored by accelerated molecular dynamics. Phys Chem Chem Phys, 16(14): 6398 – 6406. (Abstract | PDF)
  21. Miao Y*, Nichols SE, McCammon JA (2014) Mapping of Allosteric Druggable Sites in Activation-Associated Conformers of the M2 Muscarinic Receptor. Chem Bio Drug Des, 83(2): 237-246. (Abstract | PDF)
  22. Miao Y*, Nichols SE, Gasper PM, Metzger VT, McCammon JA (2013) Activation and dynamic network of the M2 muscarinic receptor. Proc Natl Acad Sci U S A 110(27): 10982-10987. (Abstract | PDF)
    • Recommended by “Faculty of 1000
    • Invited Talk, 2015 American Chemical Society Meeting (2015)
    • Invited Talk, 95th AAAS Annual Meeting (2014)
    • Invited Talk, CECAM Workshop (2014)
    • Invited Talk, Beijing Computational Science Research Center (2014)
    • Invited Talk, UCSD Mathematics and Biochemistry-Biophysics Seminar (2013)
    • Invited Talk, 57th Annual Biophysical Society Meeting (2013)
  23. Sinko W., Miao Y., de Oliveira CAF, McCammon J. A. (2013) Population Based Reweighting of Scaled Molecular Dynamics. J. Phys. Chem. B, 117(42): 12759–12768. (Abstract | PDF) (Peter Wolynes Festschrift issue)
  24. Miao, Y., L. Hong, Z. Yi and J. C. Smith (2012), Zaccai Resilience and Site-specific Hydration in a Globular Protein, Eur. Phys. J. E, 36(7): 72. (Abstract | PDF).
    • Cover Highlight: “Topical Issue on Neutron Biological Physics”
  25. Miao, Y., Z. Yi, D. Glass, L. Hong, M. Tyagi, J. Baudry, N. Jain and J. C. Smith (2012), Temperature-dependent Dynamical Transitions of Different Classes of Amino Acid Residue in a Globular Protein, J. Am. Chem. Soc., 134(48): 19576-19579. (Abstract | PDF)
    • JACS Spotlights: “Warming Proteins from the Inside Out”
  26. Miao, Y., Z. Yi, C. Cantrell, D. Glass, J. Baudry, N. Jain and J. C. Smith (2012), Coupled Flexibility Change in Cytochrome P450cam Substrate Binding Determined by Neutron Scattering, NMR and Molecular Dynamics Simulation, Biophysical J., 103(10): 2167-2176. (Abstract | PDF)
    • Press release: “Three UT Professors Combine ORNL Neutrons with UT Knoxville Superconducting Magnet and Supercomputing to Probe Enzyme Function”
  27. Yi, Z., Y. Miao, N. Jain, J. Baudry and J. C. Smith (2012), Derivation of Mean-Square Displacements for Protein Dynamics from Elastic Incoherent Neutron Scattering, J. Phys. Chem. B, 116(16):5028-5036. (Abstract | PDF)
  28. Singharoy A., H. Joshi, Y. Miao* and P. J. Ortoleva (2012), Space Warping Order Parameters and Symmetry: Application to Multiscale Simulation of Macromolecular Assemblies, J. Phys. Chem. B, 116(29):8335-8336. (Abstract | PDF)
  29. Miao, Y. and J. Baudry (2011), Active-Site Hydration and Water Diffusion in Cytochrome P450cam: a Highly Dynamic Process, Biophysical J., 101(6): 1493-1503. (Abstract | PDF)
    • Press release: “Supercomputer reveals new details behind drug-processing protein model”
  30. Miao, Y., J. E. Johnson and P. J. Ortoleva (2010), All-atom Multiscale Simulation of CCMV Capsid Swelling, J. Phys. Chem. B, 114(34), 11181–11195. (Abstract | PDF)
  31. Miao, Y. and P. J. Ortoleva (2009), Viral Structural Transition Mechanisms Revealed by Multiscale Molecular Dynamics/Order Parameter eXtrapolation Simulation, Biopoplymers, 93, 61. (Abstract | PDF)
    • Cover Highlight
  32. Pankavich, S., Z. Shreif, Y. Miao, P. J. Ortoleva (2009). Self-Assembly of Nanocomponents into Composite Structures: Derivation and Simulation of a Langevin Model. J. Chem. Phys., 130(19): 194115. (Abstract | PDF)
  33. Pankavich, S., Y. Miao, J. Ortoleva, Z. Shreif, P. Ortoleva, Stochastic Dynamics of Bionanosystems: Multiscale Analysis and Specialized Ensembles. J. Chem. Phys., 2008, 128, 234908. (Abstract | PDF)
    • Selected by Virtual Journal of Biological Physics Research
  34. Miao, Y. and P. J. Ortoleva, Molecular dynamics/order parameter extrapolation for bionanosystem simulations. J. Comp. Chem., 2008, 30(3): 423-437. (Abstract | PDF)
  35. Sayyed-Ahmad, A., Y. Miao, and P. J. Ortoleva (2007), Poisson-Boltzmann Theory for Bionanosystems. Communications in Computational Physics, 3(5): 1100. (Abstract | PDF)
  36. Huang, J., Q. Li, X. Wu, Y. Miao, J. Yang (2007), Transport Property of Two Isoelectronic Molecules. International Journal of Nanoscience, 5(6): 841-846. (Abstract | PDF)
  37. Y. Miao and P. J. Ortoleva (2006). Viral structural transitions: An all-atom multiscale theory. J. Chem. Phys., 125, 214901. (Abstract | PDF)
    • Selected by Virtual Journal of Nanoscale Science & Technology
  38. Y. Miao and P. J. Ortoleva (2006). All-Atom Multiscaling and New Ensembles for Dynamical Nanoparticles. J. Chem. Phys., 125, 044901. (Abstract | PDF)
    • Selected by Virtual Journal of Biological Physics Research

Reviews and Book Chapters

  1. Y. Miao and J. A. McCammon (2017), Gaussian Accelerated Molecular Dynamics: Theory, Implementation and Applications. David Dixon (editor), Annual Reports in Computational Chemistry, DOI: 10.1016/bs.arcc.2017.06.005. (Abstract | PDF)
  2. Miao, Y.* and McCammon, J. A. (2016). G-protein coupled receptors: advances in simulation and drug discovery. Curr Opin Struct Biol 41: 83-89. (Abstract | PDF)
  3. Miao, Y.* and McCammon JA (2016) Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review. Molecular Simulation, 42: 1046-1055.
    • Cover Highlight
    • Free access to fulltext for the first 50
  4. Vural, D., X. Hu, B. Lindner, N. Jain, Y. Miao, X. Cheng, Z. Liu, L. Hong, J. C. Smith (2016), Quasielastic Neutron Scattering in Biology: Theory and Applications, Biochimica et Biophysica Acta (BBA)-General Subjects, Biochimica et Biophysica Acta (BBA)-General Subjects, 1861 (1), 3638-3650. (Abstract | PDF)
  5. Singharoy A., H. Joshi, S. Cheluvaraja, Y. Miao, D. Brown and P. J. Ortoleva (2012), Simulating Microbial Systems: Addressing Model Uncertainty/Incompleteness via Multiscale and Entropy Methods. A. Navid (editor), Microbial Systems Biology: Methods and Protocols, Humana Press, USA, 881: 433-467. (Abstract | PDF)