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Osamu Miyashita
Osamu Miyashita
Senior Scientist, RIKEN Center for Computational Science
Verified email at riken.go.jp
Title
Cited by
Cited by
Year
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
5662003
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
3382007
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
2642004
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
2602004
Vibrational energy transfer in a protein molecule
K Moritsugu, O Miyashita, A Kidera
Physical review letters 85 (18), 3970, 2000
1802000
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
1312005
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
1132005
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
922018
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
852014
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
822003
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
722005
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
702008
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
642004
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
542017
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
542010
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
492004
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
482011
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
472009
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
462003
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
342022
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