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Osamu Miyashita - Publications

Affiliations: 
2006-2013 Chemistry University of Arizona, Tucson, AZ 
 2013- RIKEN 
Area:
General Biophysics, Biochemistry
Website:
http://www.riken.jp/TMS2012/cbp/en/member/profile/osamu_miyashita.html
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55 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
2023 Miyashita O, Tama F. Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches. Current Opinion in Structural Biology. 82: 102653. PMID 37451233 DOI: 10.1016/j.sbi.2023.102653  0.363
2023 Vuillemot R, Mirzaei A, Harastani M, Hamitouche I, Fréchin L, Klaholz BP, Miyashita O, Tama F, Rouiller I, Jonic S. MDSPACE: Extracting Continuous Conformational Landscapes from Cryo-EM Single Particle Datasets Using 3D-to-2D Flexible Fitting based on Molecular Dynamics Simulation. Journal of Molecular Biology. 167951. PMID 36638910 DOI: 10.1016/j.jmb.2023.167951  0.301
2022 Asi H, Dasgupta B, Nagai T, Miyashita O, Tama F. A hybrid approach to study large conformational transitions of biomolecules from single particle XFEL diffraction data. Frontiers in Molecular Biosciences. 9: 913860. PMID 36660427 DOI: 10.3389/fmolb.2022.913860  0.407
2022 Nakata K, Miyazaki N, Yamaguchi H, Hirose M, Kashiwagi T, Kutumbarao NHV, Miyashita O, Tama F, Miyano H, Mizukoshi T, Iwasaki K. High-resolution structure of phosphoketolase from Bifidobacterium longum determined by cryo-EM single-particle analysis. Journal of Structural Biology. 214: 107842. PMID 35181457 DOI: 10.1016/j.jsb.2022.107842  0.39
2021 Dasgupta B, Miyashita O, Uchihashi T, Tama F. Reconstruction of Three-Dimensional Conformations of Bacterial ClpB from High-Speed Atomic-Force-Microscopy Images. Frontiers in Molecular Biosciences. 8: 704274. PMID 34422905 DOI: 10.3389/fmolb.2021.704274  0.325
2020 Srivastava A, Tiwari SP, Miyashita O, Tama F. Integrative/Hybrid Modeling Approaches for Studying Biomolecules. Journal of Molecular Biology. PMID 32061933 DOI: 10.1016/J.Jmb.2020.01.039  0.36
2020 Tiwari SP, Chhabra S, Tama F, Miyashita O. Computational protocol for assessing the optimal pixel size to improve the accuracy of single particle cryo-electron microscopy maps. Journal of Chemical Information and Modeling. PMID 32003995 DOI: 10.1021/Acs.Jcim.9B01107  0.319
2019 Nakano M, Miyashita O, Tama F. Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matching. Biophysics and Physicobiology. 16: 367-376. PMID 31984191 DOI: 10.2142/Biophysico.16.0_367  0.351
2019 Dasgupta B, Miyashita O, Tama F. Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images. Biochimica Et Biophysica Acta. General Subjects. 129420. PMID 31472175 DOI: 10.1016/J.Bbagen.2019.129420  0.34
2019 Bala S, Shinya S, Srivastava A, Ishikawa M, Shimada A, Kobayashi N, Kojima C, Tama F, Miyashita O, Kohda D. Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study. Biochimica Et Biophysica Acta. General Subjects. 129418. PMID 31449839 DOI: 10.1016/J.Bbagen.2019.129418  0.529
2019 Srivastava A, Bala S, Motomura H, Kohda D, Tama F, Miyashita O. Conformational ensemble of an intrinsically flexible loop in mitochondrial import protein Tim21 studied by modeling and molecular dynamics simulations. Biochimica Et Biophysica Acta. General Subjects. 129417. PMID 31445064 DOI: 10.1016/J.Bbagen.2019.129417  0.489
2019 Nagai T, Tama F, Miyashita O. Cryo-Cooling Effect on DHFR Crystal Studied by Replica-Exchange Molecular Dynamics Simulations. Biophysical Journal. 116: 395-405. PMID 30638963 DOI: 10.1016/J.Bpj.2018.11.3139  0.469
2018 Miyashita O, Tama F. Hybrid Methods for Macromolecular Modeling by Molecular Mechanics Simulations with Experimental Data. Advances in Experimental Medicine and Biology. 1105: 199-217. PMID 30617831 DOI: 10.1007/978-981-13-2200-6_13  0.4
2018 Nagai T, Mochizuki Y, Joti Y, Tama F, Miyashita O. Gaussian mixture model for coarse-grained modeling from XFEL. Optics Express. 26: 26734-26749. PMID 30469754 DOI: 10.1364/Oe.26.026734  0.39
2018 Srivastava A, Nagai T, Srivastava A, Miyashita O, Tama F. Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics. International Journal of Molecular Sciences. 19. PMID 30380757 DOI: 10.3390/Ijms19113401  0.433
2018 Srivastava A, Tama F, Kohda D, Miyashita O. Computational Investigation of the Conformational Dynamics in Tom20-Mitochondrial Presequence Tethered Complexes. Proteins. PMID 30367523 DOI: 10.1002/Prot.25625  0.445
2018 Mori T, Kulik M, Miyashita O, Jung J, Tama F, Sugita Y. Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning. Structure (London, England : 1993). PMID 30344106 DOI: 10.1016/J.Str.2018.09.004  0.37
2018 Tiwari SP, Tama F, Miyashita O. Searching for 3D structural models from a library of biological shapes using a few 2D experimental images. Bmc Bioinformatics. 19: 320. PMID 30208849 DOI: 10.1186/S12859-018-2358-0  0.301
2018 Nakano M, Miyashita O, Jonic S, Tokuhisa A, Tama F. Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution. Journal of Synchrotron Radiation. 25: 1010-1021. PMID 29979162 DOI: 10.1107/S1600577518005568  0.384
2018 Jin Q, Miyashita O, Tama F, Yang J, Jonic S. Poisson image denoising by piecewise principal component analysis and its application in single-particle X-ray diffraction imaging Iet Image Processing. 12: 2264-2274. DOI: 10.1049/Iet-Ipr.2018.5145  0.318
2017 Nakano M, Miyashita O, Jonic S, Song C, Nam D, Joti Y, Tama F. Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL. Journal of Synchrotron Radiation. 24: 727-737. PMID 28664878 DOI: 10.1107/S1600577517007767  0.39
2017 Miyashita O, Joti Y. X-ray free electron laser single-particle analysis for biological systems. Current Opinion in Structural Biology. PMID 28501339 DOI: 10.1016/J.Sbi.2017.03.014  0.342
2017 Miyashita O, Kobayashi C, Mori T, Sugita Y, Tama F. Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations. Journal of Computational Chemistry. PMID 28370077 DOI: 10.1002/Jcc.24785  0.444
2017 Ahlstrom LS, Vorontsov II, Shi J, Miyashita O. Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations. Plos One. 12: e0170337. PMID 28107510 DOI: 10.1371/Journal.Pone.0170337  0.772
2017 MIYASHITA O, TAMA F. Hybrid Approach for Biological Structure Modeling: Cryo-electron Microscopy and X-ray Free Electron Laser Data Seibutsu Butsuri. 57: 090-094. DOI: 10.2142/Biophys.57.090  0.325
2016 Tokuhisa A, Jonic S, Tama F, Miyashita O. Hybrid approach for structural modeling of biological systems from X-ray free electron laser diffraction patterns. Journal of Structural Biology. PMID 26972893 DOI: 10.1016/J.Jsb.2016.03.009  0.46
2015 Nakano M, Tateishi-Karimata H, Tanaka S, Tama F, Miyashita O, Nakano SI, Sugimoto N. Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory. Nucleic Acids Research. PMID 26538600 DOI: 10.1093/Nar/Gkv1133  0.332
2014 Gallagher-Jones M, Bessho Y, Kim S, Park J, Kim S, Nam D, Kim C, Kim Y, Noh do Y, Miyashita O, Tama F, Joti Y, Kameshima T, Hatsui T, Tono K, et al. Macromolecular structures probed by combining single-shot free-electron laser diffraction with synchrotron coherent X-ray imaging. Nature Communications. 5: 3798. PMID 24786694 DOI: 10.1038/Ncomms4798  0.371
2014 Ahlstrom LS, Miyashita O. Packing interface energetics in different crystal forms of the λ Cro dimer. Proteins. 82: 1128-41. PMID 24218107 DOI: 10.1002/Prot.24478  0.752
2014 Tokuhisa A, Miyashita O, Tama F. 3P084 Examination of ab initio structural modeling for the pattern matching method using X-ray free electron laser(01E. Protein: Measurement & Analysis,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) Seibutsu Butsuri. 54: S262. DOI: 10.2142/Biophys.54.S262_6  0.363
2013 Ahlstrom LS, Baker JL, Ehrlich K, Campbell ZT, Patel S, Vorontsov II, Tama F, Miyashita O. Network visualization of conformational sampling during molecular dynamics simulation. Journal of Molecular Graphics & Modelling. 46: 140-9. PMID 24211466 DOI: 10.1016/J.Jmgm.2013.10.003  0.714
2013 Tokuhisa A, Miyashita O, Tama F. 2P077 Methodology of a single biomolecular structure determination for low-resolution data set obtained by X-ray Free Electron Laser(01E. Protein: Measurement & Analysis,Poster) Seibutsu Butsuri. 53: S171. DOI: 10.2142/Biophys.53.S171_5  0.369
2013 Ahlstrom LS, Miyashita O. Comparison of a simulated λ Cro dimer conformational ensemble to its NMR models International Journal of Quantum Chemistry. 113: 518-524. DOI: 10.1002/Qua.24029  0.777
2012 Ahlstrom LS, Miyashita O. Effect of Crystal Packing on Cro Dimer Conformation Biophysical Journal. 102: 45a. DOI: 10.1016/J.Bpj.2011.11.278  0.792
2011 Ahlstrom LS, Miyashita O. Molecular simulation uncovers the conformational space of the λ Cro dimer in solution. Biophysical Journal. 101: 2516-24. PMID 22098751 DOI: 10.1016/J.Bpj.2011.10.016  0.778
2011 Vorontsov II, Miyashita O. Crystal molecular dynamics simulations to speed up MM/PB(GB)SA evaluation of binding free energies of di-mannose deoxy analogs with P51G-m4-Cyanovirin-N. Journal of Computational Chemistry. 32: 1043-53. PMID 20949512 DOI: 10.1002/Jcc.21683  0.504
2011 Miyashita O, Gorba C, Tama F. Structure modeling from small angle X-ray scattering data with elastic network normal mode analysis. Journal of Structural Biology. 173: 451-60. PMID 20850542 DOI: 10.1016/J.Jsb.2010.09.008  0.464
2011 Ahlstrom LS, Miyashita O. Adding Dynamical Insight to X-Ray Images by Solution and Crystal Molecular Dynamics Simulation Biophysical Journal. 100: 377a. DOI: 10.1016/J.Bpj.2010.12.2245  0.786
2010 Campbell ZT, Baldwin TO, Miyashita O. Analysis of the bacterial luciferase mobile loop by replica-exchange molecular dynamics. Biophysical Journal. 99: 4012-9. PMID 21156144 DOI: 10.1016/J.Bpj.2010.11.001  0.483
2010 Grubisic I, Shokhirev MN, Orzechowski M, Miyashita O, Tama F. Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps. Journal of Structural Biology. 169: 95-105. PMID 19800974 DOI: 10.1016/J.Jsb.2009.09.010  0.474
2010 Vorontsov II, Miyashita O. Use of Crystal MD Simulations to Speed Up Evaluation of Binding Free Energies of Dimannose Deoxy Analogs With M4-P51g-Cyanovirin-N Biophysical Journal. 98: 39a-40a. DOI: 10.1016/J.Bpj.2009.12.228  0.5
2010 Ahlstrom LS, Miyashita O. Comparison of λ Cro Solution Ensemble To Its Open and Closed Crystal Forms Biophysical Journal. 98: 28a. DOI: 10.1016/J.Bpj.2009.12.165  0.774
2009 Vorontsov II, Miyashita O. Solution and crystal molecular dynamics simulation study of m4-cyanovirin-N mutants complexed with di-mannose. Biophysical Journal. 97: 2532-40. PMID 19883596 DOI: 10.1016/J.Bpj.2009.08.011  0.54
2008 Gorba C, Miyashita O, Tama F. Normal-mode flexible fitting of high-resolution structure of biological molecules toward one-dimensional low-resolution data. Biophysical Journal. 94: 1589-99. PMID 17993489 DOI: 10.1529/Biophysj.107.122218  0.408
2007 Whitford PC, Miyashita O, Levy Y, Onuchic JN. Conformational transitions of adenylate kinase: switching by cracking. Journal of Molecular Biology. 366: 1661-71. PMID 17217965 DOI: 10.1016/J.Jmb.2006.11.085  0.439
2006 Onuchic JN, Kobayashi C, Miyashita O, Jennings P, Baldridge KK. Exploring biomolecular machines: energy landscape control of biological reactions. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361: 1439-43. PMID 16873130 DOI: 10.1098/Rstb.2006.1876  0.363
2005 Miyashita O, Wolynes PG, Onuchic JN. Simple energy landscape model for the kinetics of functional transitions in proteins. The Journal of Physical Chemistry. B. 109: 1959-69. PMID 16851180 DOI: 10.1021/Jp046736Q  0.584
2005 Miyashita O, Okamura MY, Onuchic JN. Interprotein electron transfer from cytochrome c2 to photosynthetic reaction center: Tunneling across an aqueous interface Proceedings of the National Academy of Sciences of the United States of America. 102: 3558-3563. PMID 15738426 DOI: 10.1073/Pnas.0409600102  0.347
2004 Miyashita O, Onuchic JN, Okamura MY. Transition state and encounter complex for fast association of cytochrome c2 with bacterial reaction center Proceedings of the National Academy of Sciences of the United States of America. 101: 16174-16179. PMID 15520377 DOI: 10.1073/Pnas.0405745101  0.383
2004 Tama F, Miyashita O, Brooks CL. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. Journal of Structural Biology. 147: 315-26. PMID 15450300 DOI: 10.1016/J.Jsb.2004.03.002  0.348
2004 Tama F, Miyashita O, Brooks CL. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. Journal of Molecular Biology. 337: 985-99. PMID 15033365 DOI: 10.1016/J.Jmb.2004.01.048  0.357
2003 Miyashita O, Onuchic JN, Wolynes PG. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proceedings of the National Academy of Sciences of the United States of America. 100: 12570-5. PMID 14566052 DOI: 10.1073/Pnas.2135471100  0.525
2003 Miyashita O, Onuchic JN, Okamura MY. Continuum electrostatic model for the binding of cytochrome c2 to the photosynthetic reaction center from Rhodobacter sphaeroides Biochemistry. 42: 11651-11660. PMID 14529275 DOI: 10.1021/Bi0350250  0.367
2003 Miyashita O, Okamura MY, Onuchic JN. Theoretical understanding of the interprotein electron transfer between cytochrome c2 and the photosynthetic reaction center Journal of Physical Chemistry B. 107: 1230-1241. DOI: 10.1021/Jp026753K  0.381
2000 Tama F, Miyashita O, Kitao A, Go N. Molecular dynamics simulation shows large volume fluctuations of proteins European Biophysics Journal. 29: 472-480. PMID 11156288 DOI: 10.1007/S002490000103  0.387
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