Osamu Miyashita
Osamu Miyashita
Senior Scientist, RIKEN Center for Computational Science
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Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
O Miyashita, JN Onuchic, PG Wolynes
Proceedings of the National Academy of Sciences 100 (22), 12570-12575, 2003
Conformational transitions of adenylate kinase: switching by cracking
PC Whitford, O Miyashita, Y Levy, JN Onuchic
Journal of molecular biology 366 (5), 1661-1671, 2007
Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM
F Tama, O Miyashita, CL Brooks Iii
Journal of structural biology 147 (3), 315-326, 2004
Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis
F Tama, O Miyashita, CL Brooks III
Journal of molecular biology 337 (4), 985-999, 2004
Vibrational energy transfer in a protein molecule
K Moritsugu, O Miyashita, A Kidera
Physical review letters 85 (18), 3970, 2000
Simple energy landscape model for the kinetics of functional transitions in proteins
O Miyashita, PG Wolynes, JN Onuchic
The journal of physical chemistry B 109 (5), 1959-1969, 2005
Interprotein electron transfer from cytochrome c2 to photosynthetic reaction center: Tunneling across an aqueous interface
O Miyashita, MY Okamura, JN Onuchic
Proceedings of the National Academy of Sciences 102 (10), 3558-3563, 2005
Role of computational methods in going beyond X-ray crystallography to explore protein structure and dynamics
A Srivastava, T Nagai, A Srivastava, O Miyashita, F Tama
International journal of molecular sciences 19 (11), 3401, 2018
Macromolecular structures probed by combining single-shot free-electron laser diffraction with synchrotron coherent X-ray imaging
M Gallagher-Jones, Y Bessho, S Kim, J Park, S Kim, D Nam, C Kim, Y Kim, ...
Nature communications 5 (1), 3798, 2014
Temperature dependence of vibrational energy transfer in a protein molecule
K Moritsugu, O Miyashita, A Kidera
The Journal of Physical Chemistry B 107 (14), 3309-3317, 2003
Coupled motions in the SH2 and kinase domains of Csk control Src phosphorylation
L Wong, SA Lieser, O Miyashita, M Miller, K Tasken, JN Onuchic, ...
Journal of molecular biology 351 (1), 131-143, 2005
Normal-mode flexible fitting of high-resolution structure of biological molecules toward one-dimensional low-resolution data
C Gorba, O Miyashita, F Tama
Biophysical journal 94 (5), 1589-1599, 2008
Transition state and encounter complex for fast association of cytochrome c2 with bacterial reaction center
O Miyashita, JN Onuchic, MY Okamura
Proceedings of the National Academy of Sciences 101 (46), 16174-16179, 2004
Flexible fitting to cryo‐EM density map using ensemble molecular dynamics simulations
O Miyashita, C Kobayashi, T Mori, Y Sugita, F Tama
Journal of computational chemistry 38 (16), 1447-1461, 2017
Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps
I Grubisic, MN Shokhirev, M Orzechowski, O Miyashita, F Tama
Journal of structural biology 169 (1), 95-105, 2010
Dynamic coupling between the SH2 domain and active site of the COOH terminal Src kinase, Csk
L Wong, S Lieser, B Chie-Leon, O Miyashita, B Aubol, J Shaffer, ...
Journal of molecular biology 341 (1), 93-106, 2004
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
II Vorontsov, O Miyashita
Journal of computational chemistry 32 (6), 1043-1053, 2011
Solution and crystal molecular dynamics simulation study of m4-cyanovirin-N mutants complexed with di-mannose
II Vorontsov, O Miyashita
Biophysical journal 97 (9), 2532-2540, 2009
Continuum electrostatic model for the binding of cytochrome c 2 to the photosynthetic reaction center from Rhodobacter sphaeroides
O Miyashita, JN Onuchic, MY Okamura
Biochemistry 42 (40), 11651-11660, 2003
NMMD: Efficient cryo-EM flexible fitting based on simultaneous Normal Mode and Molecular Dynamics atomic displacements
R Vuillemot, O Miyashita, F Tama, I Rouiller, S Jonic
Journal of Molecular Biology 434 (7), 167483, 2022
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