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Yinglong Miao, Ph.D. - Publications

Affiliations: 
2009 Chemistry Indiana University, Bloomington, Bloomington, IN, United States 
Area:
systems biology, physical chemistry
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67 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Miao Y, Bhattarai A, Wang J. Ligand Gaussian accelerated molecular dynamics (LiGaMD): Characterization of ligand binding thermodynamics and kinetics. Journal of Chemical Theory and Computation. PMID 32692556 DOI: 10.1021/Acs.Jctc.0C00395  0.37
2020 Bhattarai A, Devkota S, Bhattarai S, Wolfe MS, Miao Y. Mechanisms of γ-Secretase Activation and Substrate Processing. Acs Central Science. 6: 969-983. PMID 32607444 DOI: 10.1021/Acscentsci.0C00296  0.337
2020 Pawnikar S, Miao Y. Pathway and mechanism of drug binding to chemokine receptors revealed by accelerated molecular simulations. Future Medicinal Chemistry. PMID 32515227 DOI: 10.4155/Fmc-2020-0044  0.358
2020 Bhattarai A, Wang J, Miao Y. Retrospective ensemble docking of allosteric modulators in an adenosine G-protein-coupled receptor. Biochimica Et Biophysica Acta. General Subjects. 129615. PMID 32298791 DOI: 10.1016/J.Bbagen.2020.129615  0.302
2020 Wang J, Alekseenko A, Kozakov D, Miao Y. Enhanced Sampling of Peptide Binding to Proteins through Gaussian Accelerated Molecular Dynamics Simulations Biophysical Journal. 118: 139a. DOI: 10.1016/J.Bpj.2019.11.887  0.358
2019 Wang J, Alekseenko A, Kozakov D, Miao Y. Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations. Frontiers in Molecular Biosciences. 6: 112. PMID 31737642 DOI: 10.3389/Fmolb.2019.00112  0.325
2019 Bhattarai A, Wang J, Miao Y. G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation State. Journal of Computational Chemistry. PMID 31602675 DOI: 10.1002/Jcc.26082  0.35
2019 Wang J, Miao Y. Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors. The Journal of Physical Chemistry. B. PMID 31283874 DOI: 10.1021/Acs.Jpcb.9B04867  0.373
2019 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 Central Science. 5: 651-662. PMID 31041385 DOI: 10.1021/Acscentsci.9B00020  0.309
2019 Wang J, Miao Y. Recent advances in computational studies of GPCR-G protein interactions. Advances in Protein Chemistry and Structural Biology. 116: 397-419. PMID 31036298 DOI: 10.1016/Bs.Apcsb.2018.11.011  0.317
2019 Palermo G, Gravina Ricci C, Chen JS, Miao Y, Jinek M, Doudna JA, McCammon JA. Molecular Mechanism of Off-Target Effects in CRISPR-Cas9 Biophysical Journal. 116: 319a. DOI: 10.1016/J.Bpj.2018.11.1731  0.303
2018 Huang YM, Munguia J, Miao Y, Nizet V, McCammon JA. Docking simulation and antibiotic discovery targeting the MlaC protein in Gram-negative bacteria. Chemical Biology & Drug Design. PMID 30570806 DOI: 10.1111/Cbdd.13462  0.31
2018 Miao Y, Bhattarai A, Nguyen ATN, Christopoulos A, May LT. Structural Basis for Binding of Allosteric Drug Leads in the Adenosine A Receptor. Scientific Reports. 8: 16836. PMID 30442899 DOI: 10.1038/S41598-018-35266-X  0.363
2018 Bhattarai A, Miao Y. Gaussian accelerated molecular dynamics for elucidation of drug pathways. Expert Opinion On Drug Discovery. 1-11. PMID 30371112 DOI: 10.1080/17460441.2018.1538207  0.388
2018 Miao Y. Acceleration of biomolecular kinetics in Gaussian accelerated molecular dynamics. The Journal of Chemical Physics. 149: 072308. PMID 30134710 DOI: 10.1063/1.5024217  0.43
2018 Amaro RE, Baudry J, Chodera J, Demir Ö, McCammon JA, Miao Y, Smith JC. Ensemble Docking in Drug Discovery. Biophysical Journal. PMID 29606412 DOI: 10.1016/J.Bpj.2018.02.038  0.347
2018 Miao Y, McCammon JA. Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor. Proceedings of the National Academy of Sciences of the United States of America. PMID 29507218 DOI: 10.1073/Pnas.1800756115  0.361
2018 Huang YM, McCammon JA, Miao Y. Replica exchange Gaussian accelerated molecular dynamics: Improved enhanced sampling and free energy calculation. Journal of Chemical Theory and Computation. PMID 29489349 DOI: 10.1021/Acs.Jctc.7B01226  0.327
2018 Miao Y, Huang YM, Walker RC, McCammon JA, Chang CA. Ligand Binding Pathways and Conformational Transitions of the HIV Protease. Biochemistry. PMID 29394043 DOI: 10.1021/Acs.Biochem.7B01248  0.374
2017 Miao Y, McCammon JA. Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications. Annual Reports in Computational Chemistry. 13: 231-278. PMID 29720925 DOI: 10.1016/Bs.Arcc.2017.06.005  0.444
2017 Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proceedings of the National Academy of Sciences of the United States of America. PMID 28652374 DOI: 10.1073/Pnas.1707645114  0.374
2017 Caliman AD, Miao Y, McCammon JA. Mapping the Allosteric Sites of the A2A Adenosine Receptor. Chemical Biology & Drug Design. PMID 28639411 DOI: 10.1111/Cbdd.13053  0.303
2017 Caliman AD, Miao Y, McCammon JA. Activation Mechanisms of the First Sphingosine-1-Phosphate Receptor. Protein Science : a Publication of the Protein Society. PMID 28370663 DOI: 10.1002/Pro.3165  0.322
2017 Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. CRISPR-Cas9: Computational Insights Toward Improved Genome Editing Biophysical Journal. 112: 72a. DOI: 10.1016/J.Bpj.2016.11.432  0.323
2017 Miao Y, McCammon JA. Enhanced Simulations and Drug Discovery of a Muscarinic G-Protein-Coupled Receptor Biophysical Journal. 112: 328a-329a. DOI: 10.1016/J.Bpj.2016.11.1777  0.382
2016 Pang YT, Miao Y, Wang Y, McCammon JA. Gaussian Accelerated Molecular Dynamics in NAMD. Journal of Chemical Theory and Computation. PMID 28034310 DOI: 10.1021/Acs.Jctc.6B00931  0.418
2016 Andersen OJ, Risør MW, Poulsen EC, Nielsen NC, Miao Y, Enghild JJ, Schiøtt B. The reactive center loop insertion in α-1-antitrypsin captured by accelerated molecular dynamics simulation. Biochemistry. PMID 27995800 DOI: 10.1021/Acs.Biochem.6B00839  0.386
2016 Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations. Acs Central Science. 2: 756-763. PMID 27800559 DOI: 10.1021/Acscentsci.6B00218  0.335
2016 Miao Y, McCammon JA. Graded activation and free energy landscapes of a muscarinic G-protein-coupled receptor. Proceedings of the National Academy of Sciences of the United States of America. 113: 12162-12167. PMID 27791003 DOI: 10.1073/Pnas.1614538113  0.369
2016 Miao Y, Goldfeld DA, Moo EV, Sexton PM, Christopoulos A, McCammon JA, Valant C. Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor. Proceedings of the National Academy of Sciences of the United States of America. 113: E5675-84. PMID 27601651 DOI: 10.1073/Pnas.1612353113  0.325
2016 Miao Y, McCammon JA. Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review. Molecular Simulation. 42: 1046-1055. PMID 27453631 DOI: 10.1080/08927022.2015.1121541  0.33
2016 Miao Y, McCammon JA. G-protein coupled receptors: advances in simulation and drug discovery. Current Opinion in Structural Biology. 41: 83-89. PMID 27344006 DOI: 10.1016/J.Sbi.2016.06.008  0.371
2016 Vural D, Hu X, Lindner B, Jain N, Miao Y, Cheng X, Liu Z, Hong L, Smith JC. Quasielastic neutron scattering in biology: Theory and applications. Biochimica Et Biophysica Acta. PMID 27316321 DOI: 10.1016/J.Bbagen.2016.06.015  0.345
2016 Huang YM, Miao Y, Munguia J, Lin L, Nizet V, McCammon JA. Molecular dynamic study of MlaC protein in Gram-negative bacteria: conformational flexibility, solvent effect and protein-phospholipid binding. Protein Science : a Publication of the Protein Society. 25: 1430-7. PMID 27111825 DOI: 10.1002/Pro.2939  0.34
2016 Miao Y, Baudry J, Smith JC, McCammon JA. General trends of dihedral conformational transitions in a globular protein. Proteins. 84: 501-14. PMID 26799251 DOI: 10.1002/Prot.24996  0.371
2016 Miao Y, McCammon JA. Activation of a Muscarinic G-Protein Coupled Receptor and Structure-Based Design of Allosteric Modulators Biophysical Journal. 110: 426a-427a. DOI: 10.1016/J.Bpj.2015.11.2304  0.353
2015 Kappel K, Miao Y, McCammon JA. Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor. Quarterly Reviews of Biophysics. 48: 479-87. PMID 26537408 DOI: 10.1017/S0033583515000153  0.331
2015 Miao Y, Feher VA, McCammon JA. Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation. Journal of Chemical Theory and Computation. 11: 3584-3595. PMID 26300708 DOI: 10.1021/Acs.Jctc.5B00436  0.383
2015 Miao Y, Feixas F, Eun C, McCammon JA. Accelerated molecular dynamics simulations of protein folding. Journal of Computational Chemistry. 36: 1536-49. PMID 26096263 DOI: 10.1002/Jcc.23964  0.402
2015 Miao Y, Caliman AD, McCammon JA. Allosteric effects of sodium ion binding on activation of the m3 muscarinic g-protein-coupled receptor. Biophysical Journal. 108: 1796-806. PMID 25863070 DOI: 10.1016/J.Bpj.2015.03.003  0.335
2015 Caliman AD, Swift SE, Wang Y, Miao Y, McCammon JA. Investigation of the conformational dynamics of the apo A2A adenosine receptor. Protein Science : a Publication of the Protein Society. 24: 1004-12. PMID 25761901 DOI: 10.1002/Pro.2681  0.316
2015 Ellingson SR, Miao Y, Baudry J, Smith JC. Multi-conformer ensemble docking to difficult protein targets. The Journal of Physical Chemistry. B. 119: 1026-34. PMID 25198248 DOI: 10.1021/Jp506511P  0.373
2015 Miao Y, McCammon JA. Activation and Drug Design of a Muscarinic G-Protein Coupled Receptor Biophysical Journal. 108: 95a. DOI: 10.1016/J.Bpj.2014.11.547  0.354
2014 Miao Y, Sinko W, Pierce L, Bucher D, Walker RC, McCammon JA. Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation. Journal of Chemical Theory and Computation. 10: 2677-2689. PMID 25061441 DOI: 10.1021/Ct500090Q  0.378
2014 Miao Y, Nichols SE, McCammon JA. Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics. Physical Chemistry Chemical Physics : Pccp. 16: 6398-406. PMID 24445284 DOI: 10.1039/C3Cp53962H  0.369
2014 Miao Y, Nichols SE, McCammon JA. Mapping of allosteric druggable sites in activation-associated conformers of the M2 muscarinic receptor. Chemical Biology & Drug Design. 83: 237-46. PMID 24112716 DOI: 10.1111/Cbdd.12233  0.333
2014 Miao Y, McCammon JA. Activation of the M2 Muscarinic Receptor and Computer-Aided Design of Receptor-Selective Allosteric Drugs Biophysical Journal. 106: 101a. DOI: 10.1016/J.Bpj.2013.11.630  0.332
2013 Miao Y, Hong L, Yi Z, Smith JC. Zaccai neutron resilience and site-specific hydration dynamics in a globular protein. The European Physical Journal. E, Soft Matter. 36: 72. PMID 23852576 DOI: 10.1140/Epje/I2013-13072-5  0.357
2013 Sinko W, Miao Y, de Oliveira CA, McCammon JA. Population based reweighting of scaled molecular dynamics. The Journal of Physical Chemistry. B. 117: 12759-68. PMID 23721224 DOI: 10.1021/Jp401587E  0.405
2013 Miao Y, McCammon JA. Enhanced Conformational Sampling of M2 Muscarinic Acetylcholine Receptor for Designing Selective Allosteric Drugs Biophysical Journal. 104: 26a. DOI: 10.1016/J.Bpj.2012.11.182  0.336
2012 Miao Y, Yi Z, Cantrell C, Glass DC, Baudry J, Jain N, Smith JC. Coupled flexibility change in cytochrome P450cam substrate binding determined by neutron scattering, NMR, and molecular dynamics simulation. Biophysical Journal. 103: 2167-76. PMID 23200050 DOI: 10.1016/J.Bpj.2012.10.013  0.391
2012 Singharoy A, Joshi H, Cheluvaraja S, Miao Y, Brown D, Ortoleva P. Simulating microbial systems: addressing model uncertainty/incompleteness via multiscale and entropy methods. Methods in Molecular Biology (Clifton, N.J.). 881: 433-67. PMID 22639222 DOI: 10.1007/978-1-61779-827-6_15  0.695
2012 Yi Z, Miao Y, Baudry J, Jain N, Smith JC. Derivation of mean-square displacements for protein dynamics from elastic incoherent neutron scattering. The Journal of Physical Chemistry. B. 116: 5028-36. PMID 22471396 DOI: 10.1021/Jp2102868  0.368
2012 Singharoy A, Joshi H, Miao Y, Ortoleva PJ. Space warping order parameters and symmetry: application to multiscale simulation of macromolecular assemblies. The Journal of Physical Chemistry. B. 116: 8423-34. PMID 22356532 DOI: 10.1021/Jp2119247  0.725
2012 Singharoy A, Joshi H, Miao Y, Ortoleva PJ. Space warping order parameters and symmetry: Application to multiscale simulation of macromolecular assemblies Journal of Physical Chemistry B. 116: 8423-8434. DOI: 10.1021/jp2119247  0.675
2012 Yi Z, Miao Y, Baudry J, Jain N, Smith JC. Temperature Dependent Dynamics of Cytochrome P450cam from Elastic Incoherent Neutron Scattering Biophysical Journal. 102: 382a. DOI: 10.1016/J.Bpj.2011.11.2089  0.363
2011 Miao Y, Baudry J. Active-site hydration and water diffusion in cytochrome P450cam: a highly dynamic process. Biophysical Journal. 101: 1493-503. PMID 21943431 DOI: 10.1016/J.Bpj.2011.08.020  0.311
2011 Reyles J, Miao Y, Baudry J, Smith JC. Dynamics Investigation of the Cytochrome P450cam Active Site Mutant Thr252ALA Biophysical Journal. 100: 222a. DOI: 10.1016/J.Bpj.2010.12.1423  0.314
2010 Miao Y, Johnson JE, Ortoleva PJ. All-atom multiscale simulation of cowpea chlorotic mottle virus capsid swelling. The Journal of Physical Chemistry. B. 114: 11181-95. PMID 20695471 DOI: 10.1021/Jp102314E  0.618
2010 Miao Y, Ortoleva PJ. Viral structural transition mechanisms revealed by multiscale molecular dynamics/order parameter extrapolation simulation Biopolymers. 93: 61-73. PMID 19728362 DOI: 10.1002/Bip.21299  0.639
2009 Pankavich S, Shreif Z, Miao Y, Ortoleva P. Self-assembly of nanocomponents into composite structures: derivation and simulation of Langevin equations. The Journal of Chemical Physics. 130: 194115. PMID 19466829 DOI: 10.1063/1.3134683  0.747
2009 Miao Y, Ortoleva PJ. Molecular dynamics/order parameter extrapolation for bionanosystem simulations Journal of Computational Chemistry. 30: 423-437. PMID 18636559 DOI: 10.1002/Jcc.21071  0.628
2008 Pankavich S, Miao Y, Ortoleva J, Shreif Z, Ortoleva P. Stochastic dynamics of bionanosystems: Multiscale analysis and specialized ensembles. The Journal of Chemical Physics. 128: 234908. PMID 18570529 DOI: 10.1063/1.2931572  0.764
2008 Adhangale P, Srinath C, Miao Y, Shreif Z, Ortoleva P. A multi-scale approach to bionanosystem simulation; applications to computer-aided vaccine design, nanocapsules for drug delivery and medical imaging Aiche Annual Meeting, Conference Proceedings.  0.714
2008 Sayyed-Ahmad A, Miao Y, Ortoleva P. Poisson-Boltzmann theory of bionanosystems Communications in Computational Physics. 3: 1100-1116.  0.672
2006 Miao Y, Ortoleva PJ. Viral structural transitions: An all-atom multiscale theory Journal of Chemical Physics. 125. PMID 17166043 DOI: 10.1063/1.2400858  0.594
2006 Miao Y, Ortoleva P. All-atom multiscaling and new ensembles for dynamical nanoparticles. The Journal of Chemical Physics. 125: 44901. PMID 16942186 DOI: 10.1063/1.2218838  0.584
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