Embedded Files
W. Zhao, O. Miyashita, M. Nakano and F. Tama
Xphase3d: Memory-Distributed Phase Retrieval for Reconstructing Large-Scale 3D Density Maps of Biological Macromolecules
IEEE CLUSTER, 2024
X. Wu, O Miyashita, F Tama
Modeling Conformational Transitions of Biomolecules from Atomic Force Microscopy Images using Normal Mode Analysis
J. Phys. Chem. B 2024
F Tama, J. Chen
Data Science for Integrated Dynamic Structural Biology
Biophysical Reviews 2024
Q. Wu, M. Taki, Y. Tanaka, M. Kesherwani, Q. Manh Phung, S. Enoki, Y. Okada, F. Tama, S. Yamaguchi
Angewandte Chemie 2024
W. Zhao, O Miyashita, M. Nakano, F Tama
Structure determination using high-order spatial correlations in single-particle X-ray scattering
IUCrJ 2024
O Miyashita, F Tama
Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches.
Curr. Opin. Struct. Biol. 2023
R Vuillemot, A Mirzaei, M Harastani, I Hamitouche, L Fréchin, BP Klaholz, O Miyashita, F Tama, I. Rouiller, S. Jonic
MDSPACE: Extracting continuous conformational landscapes from cryo-EM single particle datasets using 3D-to-2D flexible fitting based on Molecular Dynamics simulation
J. Mol. Biol. 2023
G Channing, R Patel, P Olaya, A Rorabaugh, O Miyashita, S Caino-Lores, C. Schuman, F. Tama, M. Taufer
Composable Workflow for Accelerating Neural Architecture Search Using In Situ Analytics for Protein Classification
Proceedings 52nd ICPP 2023
M Nakano, O Miyashita, F Tama
Molecular size dependence on achievable resolution from XFEL single-particle 3D reconstruction Structural Dynamics 2023
R. Isoda, Z. Palmai A. Yoshinari, LQ Chen, F. Tama, WB. Frommer, M. Nakamura
SWEET13 transport of sucrose, but not gibberellin, restores male fertility in Arabidopsis sweet13;14
PNAS 2022
P. Olaya, S. Caino-Lores, V. Lama, R. Patel, A. Rorabaugh, O. Miyashita, F. Tama, M. Taufer
Identifying Structural Properties of Proteins from X- ray Free Electron Laser Diffraction Patterns.
Proceedings of the 18th IEEE International Conference on e-Science (eScience) IEEE Computer Society 2022
R. Patel, A. Keller Rorabaugh, P. Olaya, S. Caino-Lores, G. Channing, C. Schuman, O. Miyashita, F. Tama, M. Taufer.
A Methodology to Generate Efficient Neural Networks for Classification of Scientific Datasets.
Proceedings of the 18th IEEE International Conference on e-Science (eScience). IEEE Computer Society (Short paper) 2022
S. Miller, M. Kesherwani, P. Chan, Y. Nagai, M. Yagi, J. Cope, F. Tama, S.A. Kay, T. Hirota
CRY2 isoform selectivity of a circadian clock modulator with anti-glioblastoma efficacy
PNAS 2022
M. Nakano, O. Miyashita Y. Joti, A. Suzuki, H. Mitomo, Y. Niida, Y. Yang, H. Yumoto, T. Koyama, K. Tono, H. Ohashi, M. Yabash, T. Ishikawa, Y. Bessho, K. Ijiro, Y. Nishino, F. Tama
Three-dimensional structure determination of gold nano triangles in solution using X-ray free-electron laser single-particle analysis
Optica 2022
H. Asi, B. Dasgupta, T. Nagai, O. Miyashita, F. Tama
A hybrid approach to study large conformational transitions of biomolecules from single particle XFEL diffraction data
Frontiers Mol. BioSci. 2022
AM Schulte, D Kolarski, V Sundaram, A Srivastava, F Tama, BL Feringa, W Szymanski
Light-Control over Casein Kinase 1δ Activity with Photopharmacology: A Clear Case for Arylazopyrazole-Based Inhibitors
Int. J. Mol. Sci. 2022
K. Nakata, N. Miyazaki, H. Yamaguchi, M. Hirose, T. Kashiwagi, N. HV Kutumbarao, O. Miyashita, F. Tama, H. Miyano, T. Mizukoshi and K. Iwasaki
J. Struct. Biol. 2022
R Vuillemot, O Miyashita, F Tama, I Rouiller and S Jonic
J. Mol. Biol. 2022
M. Kuzuya, H. Hirano, K. Hayashida, M. Watanabe, K. Kobayashi, T. Terada, Md. I. Mahmood, F. Tama, K. Tani, Y. Fujiyoshi and A. Oshima
Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N-terminus and phospholipids
Science Signalling 2022
S. Tiwari, F. Tama and O. Miyashita
Protocol for retrieving three-dimensional biological shapes for a few XFEL single particle diffraction patterns
J. Chem. Inf. Model. 2021
B. Dasgupta, O. Miyashita, T. Uchihashi and F. Tama
Reconstruction of three-dimensional conformations of bacterial ClpB from high-speed atomic- force-microscopy images
Frontiers Mol. BioSci. 2021
S. Miller, A. Srivastava, Y. Nagai, Y. Aikawa, F. Tama, and T. Hirota.
Structural differences in the FAD-binding pockets and lid loops of mammalian CRY1 and CRY2 for isoform-selective regulation
PNAS 2021
D. Kolarski, C. Miró-Vinyals, A. Sugiyama, A. Srivastava, D. Ono, Y. Nagai, M. Iida, K. Itami, F. Tama, W. Szymanski, T. Hirota & BL. Feringa
Reversible modulation of circadian time with chronophotopharmacology
Nature Communications 2021
D. Kolarski, S. Miller, T. Oshima, Y. Nagai, Y. Aoki, P. Kobauri, A. Srivastava, A. Sugiyama, K. Amaike, A. Sato, F. Tama, W. Szymanski, BL. Feringa, K. Itami & T. Hirota.
Photopharmacological Manipulation of Mammalian CRY1 for Regulation of the Circadian Clock
JACS 2021
S. Miller, YL. Son, Y. Aikawa, E. Makino, Y. Nagai, A. Srivastava, T. Oshima, A. Sugiyama, A. Hara, K. Abe, K. Hirata, S. Oishi, S. Hagihara, A. Sato, F. Tama, K. Itami, SA. Kay, M. Hatori, T. Hirota
Isoform-selective regulation of mammalian cryptochromes
Nature Chemical Biology 2020
Image by Issey Takahashi, Nagoya University
JL Fribourgh, A. Srivastava, CR Sandate, AK Michael, PL Hsu, C. Rakers, LT Nguyen, MR Torgrimson, GC G Parico, S. Tripathi, N. Zheng, GC Lander, T. Hirota, F. Tama & CL Partch.
Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK: BMAL1 to control circadian timing.
eLife 2020
S. Tiwari, S. Chhabra, F. Tama & O. Miyashita.
Computational protocol for assessing the optimal pixel size to improve the accuracy of single particle cryo-electron microscopy maps.
J. Chem. Inf. Model. 2020
A. Srivastava, SP Tiwari, O. Miyashita & F. Tama
Integrative/Hybrid Modeling Approaches for Studying Biomolecules.
J. Mol. Biol. 2020
B. Dasgupta, O. Miyashita & F. Tama.
Reconstruction of Low-resolution Molecular Structures from Simulated Atomic Force Microscopy Images.
BBA – General Subjects 2020
S. Bala, S. Shinya, A. Srivastava, M. Ishikawa, A. Shimada, N. Kobayashi, C. Kojima, F. Tama, O. Miyashita & D. Kohda.
Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study.
BBA – General Subjects 2020
A. Srivastava, S. Bala, H. Motomura, D. Kohda, F. Tama & O. Miyashita.
Conformational ensemble of an intrinsically flexible loop in mitochondrial import protein Tim21 studied by modeling and molecular dynamics simulations.
BBA – General Subjects 2020
D. Kolarski, A. Sugiyama, G. Breton, C. Rakers, D. Ono, A. Schulte, F. Tama, K. Itami, W. Szymanski, T. Hirota & B. Feringa.
Controlling the Circadian Clock with High Temporal Resolution through Photodosing.
JACS 2019
Image by Issei Takahashi, Nagoya University
A. Putarjunan, J. Ruble, A. Srivastava, C. Zhao, A. Rychel, A. Hofstetter, X. Tang, JK Zhu, F. Tama, N. Zheng & K. Torii.
Bipartite anchoring of SCREAM enforces stomatal initiation by coupling MAP Kinases to SPEECHLESS.
Nature Plants 2019
M. Nakano, O. Miyashita & F. Tama. Parameter Optimization for 3D-Reconstruction from XFEL Diffraction Patterns Based on Fourier Slice Matching. Biophysics and Physicobiology 2019
T. Nagai, F. Tama & O. Miyashita.
Cryo-cooling effect on DHFR crystal studied by replica-exchange molecular dynamics simulations.
Biophysical J. 2019
A. Oshima, Y. Niwa, K. Kuwata, A. Srivastava, T. Hyoda, Y. Tsuchiya, M. Kumagai, M. Tsuyuguchi, T. Tamaru, A. Sugiyama, N. Ono, N. Zolboot, Y. Aikawa, S. Oishi, A. Nonami, F. Arai, S. Hagihara, J. Yamaguchi, F. Tama, Y. Kunisaki, K. Yagita, M. Ikeda5, T. Kinoshita, S.A. Kay, K. Itami & T. Hirota.
Cell-based screen identifies a new potent and highly selective CK2 inhibitor for modulation of circadian rhythms and cancer cell growth.
Science Advances 2019
T. Mori, M. Kulik, O. Miyashita, J. Jung, F. Tama and Y. Sugita.
Acceleration of cryo-EM flexible fitting by efficient space partitioning for large biomolecular systems.
Structure 2019
A. Srivastava, F. Tama, D. Kohda & O.Miyashita.
Computational Investigation of the Conformational Dynamics in Tom20-Mitochondrial Presequence Tethered Complexes.
Proteins 2019
A. Srivastava, T. Nagai, A. Srivastava, O. Miyashita & F. Tama.
Role of computational methods in going beyond X-ray crystallography to explore protein structure and dynamics.
Int. J. Mol. Sci. 2018
O. Miyashita & F. Tama
Hybrid Methods for Macromolecular Modeling by Molecular Mechanics Simulations with Experimental Data.
In: Nakamura H., Kleywegt G., Burley S., Markley J. (eds) Integrative Structural Biology with Hybrid Methods. Advances in Experimental Medicine and Biology 2018
T. Nagai, Y. Mochizuki, Y. Joti, F. Tama & O. Miyashita.
Gaussian mixture model for coarse-grained modeling from XFEL.
Optics Express 2018
S. P. Tiwari, F. Tama & O. Miyashita.
Searching for 3D structural models from a library of biological shapes using a few 2D experimental images.
BMC Bioinformatics 2018
Q. Jin, O. Miyashita, F. Tama, J. Yang & S. Jonic.
Poisson image denoising by piecewise principal component analysis and its application in single-particle X-ray diffraction imaging,
IET Image Processing 2018
M. Nakano, O. Miyashita, S. Jonic, A. Tokuhisa, F. Tama.
Single-particle XFEL 3D Reconstruction of Ribosome-size Particles based on Fourier Slice Matching: Requirements to Reach Subnanometer Resolution.
J. Synchrotron Rad. 2018
A. Srivastava, T. Hirota, S. Irle and F. Tama.
Conformational dynamics of human Protein Kinase CK2α and its effect on function and inhibition.
Proteins. 2018
M. Nakano, O. Miyashita, S. Jonic, C. Song, D. Nam, Y. Joti and F. Tama.
Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL.
J. Synchrotron Rad. 2017
T. Shimizu and F. Tama.
Editorial overview: Macromolecular assemblies.
Curr. Opin. Struc. Biol. 2017
O. Miyashita, C. Kobayashi, T. Mori, Y. Sugita, F. Tama.
Flexible Fitting to Cryo-EM Density Map using Ensemble Molecular Dynamics Simulations.
J. Comp. Chem.2017
O. Miyashita and F. Tama.
Hybrid approach for biological structure modeling: cryo-electron microscopy and X-ray free electron laser data.
Seibutsu Butsuri 2017
M. Nakano, H. Tateishi-Karimata, S. Tanaka, F. Tama, O. Miyashita, S. Nakano, N. Sugimoto.
Local thermodynamics of the water molecules around single- and double-stranded DNA studied by grid inhomogeneous salvation theory.
Chem. Phys. Lett. 2016
A. Tokuhisa, S. Jonic; F. Tama and O. Miyashita.
Hybrid Approach for Structural Modeling of Biological Systems from X-ray Free Electron Laser Diffraction Patterns.
J. Struct. Biol. 2016
M. Nakano, H. Tateishi-Karimata, S. Tanaka, F. Tama, O. Miyashita, S. Nakano, N. Sugimoto.
Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory.
Nucleic Acids Res. 2015 43(21): 10114-25
Q. Jin, Q., C.O.Sanchez Soriano, J.M. de la Rosa-Trevin, F. Tama, and S. Jonic.
Macromolecular Dynamics by Hybrid Electron Microscopy Normal Mode Analysis
Microscopy and Microanalysis
2014 20:1218-19
Q. Jin, C.O. Sanchez Sorzano, I. Callebaut, F. Tama, S. Jonic.
Elastic image registration to fully explore macromolecular dynamics by electron microscopy.
In: Image Processing (ICIP), 2014 IEEE International Conference, 2014
C.O. Sorzano, J.M. de la Rosa-Trevín, F. Tama, S. Jonić.
Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol.
J. Struct. Biol. 2014188:134-41
S. Patel, E. Vierling and F. Tama.
Replica exchange molecular dynamics simulations provide insight into substrate recognition by small heat shock proteins.
Biophys J. 2014 10:2644-55
J. Lega, S. Buxner, B. Blonder and F. Tama
Exploration in integrated sciences
J. Coll. Sci. Teach. 2014
JR Lopez-Blanco, O. Miyashita, F. Tama and P. Chacon
Normal Mode Analysis Techniques in Structural Biology.
In: eLS. John Wiley & Sons, Ltd: Chichester. 2014
M. Gallagher-Jones, Y. Bessho, S. Kim, J. Park, S. Kim, D. Nam, C. Kim, Y. Kim, Y. Noh do, O. Miyashita, F. Tama, Y. Joti, T. Kameshima, T. Hatsui, K. Tono, Y. Kohmura, M. Yabashi, SS. Hasnain, T. Ishikawa, C. Song.
Macromolecular structures probed by combining single-shot free-electron laser diffraction with synchrotron coherent X-ray imaging.
Nat Commun. 2014 2:5:3798
Q Jin, CO Sorzano, JM de la Rosa-Trevín, JR Bilbao-Castro, R. Núñez-Ramírez, O. Llorca , F. Tama, S. Jonić.
Iterative elastic 3D-to-2D alignment method using normal modes for studying structural dynamics of large macromolecular complexes.
Structure 2014 22:496-506
L. Ashtrom, J. Baker, K. Ehrlich, Z. Campbell, S. Patel, I. Vorontsov, F. Tama, O. Miyashita.
Network Visualization of Conformational Sampling during Molecular Dynamics Simulation.
J. Mol. Graph. Mod. 2013 46:140-9
Lyumkis, H. Talley, A. Stewart, S. Shah, CK. Park, F. Tama, CS Potter, B. Carragher, NC. Horton.
Allosteric Regulation of DNA Cleavage and Sequence-Specificity through Run-On Oligomerization.
Structure 2013 8:21:1848-58
Nogales-Cadenas, S. Jonic, F. Tama, A. Arteni, D. Tabas-Madrid, M. Vazquez, A. Pascual-Montano, CO. Sorzano.
3DEM Loupe: analysis of macromolecular dynamics using structures from electron microscopy.
Nucl. Acid. Res., 2013 41:W363-W367
J. Baker, N. Biais and F. Tama.
In silico studies of Pilus IV,
Plos Computational Biology 2013 9(4):e1003032
B. Fritz, SA. Roberts, A. Ahmed, L. Breci, W. Li, A. Weichsel, JL. Brailey, VH. Wysocki, F. Tama, WR. Montfort.
Molecular Model of a Soluble Guanylyl Cyclase Fragment Determined by Small-Angle X-ray Scattering and Chemical Cross-Linking.
Biochemistry 2013 52:1568-82
A. Ahmed and F. Tama.
Consensus among multiple approaches as a reliability measure for flexible fitting into cryo-EM data.
J. Struct. Biol. 2013 182: 67-7
B.A.J. Baumann, D.W. Taylor, Z. Huang, F. Tama, P.M. Fagnant, K.M. Trybus and K. Taylor.
Phosphorylated smooth muscle heavy meromyosin shows an open conformation linked to activation,
J Mol Biol. 2012 415:274-87
A. Ahmed, P.C. Whitford, K.Y. Sanbonmatsu and F. Tama.
Consensus among flexible fitting approaches improves the interpretation of cryo-EM data,
J. Struc. Biol 2012 177:561-70
J. Baker, SH Wright and F.Tama.
Simulations of substrate transport in the multidrug transporter EmrD,
Proteins 2012 80:1620-32
Zhang, X. He, J. Baker, F. Tama, G. Chang and S.H. Wright
Twelve Transmembrane Helices form the functional core of Mammalian Mate1,
J. Biol. Chem. 2012 287:27971-82
O. Miyashita, C. Gorba and F. Tama.
Structure modeling from small angle X-ray scattering data with elastic network normal mode analysis.
J. Struc. Biol., 2011 173:451-60
P.C. Whitford, A. Ahmed, Y. Yu, S.P. Hennelly, F. Tama, C.M.T. Spahn, J.N. Onuchic and K.Y. Sanbonmatsu.
Atomic Details of Ribosomal Translocation Revealed Through Simulation Based Modeling,
Proc. Natl. Acad. Sci. USA 2011 108:18943-8
I. Grubisic, M.N. Shokhirev, M. Orzechowski, O. Miyashita and F. Tama.
Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps
J. Struc. Biol., 2010 169:95-105
Katayama, J. Wang, F. Tama, L. Chollet, E. Gogol, R Collier, M. Fisher.
Three-Dimensional Structure of the Anthrax Toxin Pore Inserted into Lipid Nanodiscs and Lipid Vesicles.
Proc. Natl. Acad. Sci. USA 2010 7:3453-7
C. Gorba and F. Tama.
Normal Mode Flexible Fitting of High-Resolution Structures of Biological Molecules Toward SAXS Data.
Bioinformatics and biology insights 2010 4:43-54
C. Gorba, O. Miyashita and F. Tama.
Computational methods for flexible fitting of high-resolution structure toward low-resolution 1 dimensional data
Biophys. J. 2010 94:1589-1599
Orzechowski and F. Tama.
Flexible fitting of high-resolution X-ray structures into cryo-electron microscopy maps using biased Molecular Dynamics simulations
Biophys. J. 2008 95: 5692-5705
R. Konecny, J. Trylska, F. Tama, D. Zhang , NA. Baker, CL. Brooks III and JA. McCammon.
Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids.
Biopolymers 2006 82: 106-120
B. Sherman, R. H. Guenther, F. Tama, T. L. Sit, CL. Brooks III, A. M. Mikhailov, E. V. Orlova, T.S. Baker and S. A. Lommel
Removal of Divalent Cations Induces Structural Transitions in Red clover necrotic mosaic virus Revealing a Potential Mechanism for RNA Release
J. Virology, 2006 80: 10395-10406
F. Tama, G. Ren, CL. Brooks III and AK. Mitra
Model of the toxic complex of anthrax : responsive conformational changes in both the lethal factor rand the protective antigen heptamer.
Protein Science, 2006 15: 2190-200
F. Tama and CL. Brooks III.
Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis.
J. Mol. Biol. 2005 345: 299-314
F. Tama, M. Feig, CL. Brooks, III and KA. Taylor.
The Requirement for Mechanical Coupling Between Head and S2 Domains in Smooth Muscle Myosin ATPase Regulation and its Implications for Dimeric Motor Function
J. Mol. Biol. 2005 345: 837-854
J. Falke, F. Tama, CL. Brooks III, EP. Gogol and MT. Fisher.
The 13 Å Structure of a Chaperonin GroEL-Protein Substrate complex by Cryo-Electron Microscopy.
J. Mol. Biol. 2005 348: 219-230
Mitra, C. Scaffitzel, T. Shaikh, F. Tama, S. Jenni, CL. Brooks III, N. Ban and J. Frank.
Structure of the E. coli protein-conducting channel bound to a translating ribosome.
Nature 2005 438: 318-324
W. Wriggers, P. Chacon, J. Kovacs, F. Tama and S. Birmanns.
Topology representing Neural Networks reconcile biomolecular shape structure and dynamics.
Neurocomputing 2004 56: 365-379
J. Trylska, R. Konecny, F. Tama, CL. Brooks III and JA McCammon.
Motions of the ribosome modulate electrostatic properties.
Biopolymers 2004 74: 423-431
F. Tama, O. Miyashita and CL. Brooks III.
NMFF: Flexible high-resolution annotation of low-resolution experimental data from cryo-EM maps using normal mode analysis.
J. Struc. Biol. 2004 147: 315-326
F. Tama, O. Miyashita and CL. Brooks, III.
Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis.
J. Mol. Biol. 2004 337: 985-999
F. Tama, M. Valle, J. Frank and CL Brooks III.
Understanding the ratchet-like inter-subunit reorganization of the ribosome.
Proc. Natl. Acad. Sci. USA 2003 100: 9319-9323
P. Chacon, F. Tama and W. Wriggers.
Mega-dalton biomolecular motion captured from electron microscopy reconstructions.
J. Mol. Biol. 2003 326: 485-492
F. Tama and CL. Brooks III.
Exploring Large-Scale Conformational Changes in Virus Maturation
.J. Mol. Biol. 2002 318: 733-747
F. Tama, W. Wriggers and CL. Brooks III. Exploring global distortions of biological macromolecules from low-resolution structural information and elastic network theory.
J. Mol. Biol. 2002 321: 297-305
F. Tama and Y.H. Sanejouand.
Conformational change of Proteins arising from Normal Mode Analysis.
Protein. Eng. 2001 14: 1-6
F. Tama, F.X. Gadea, O. Marques and Y.H. Sanejouand.
A building block approach for determining low-frequency normal modes of macromolecules.
Proteins 2000 41: 1-7
F. Tama, O. Miyashita, A. Kitao and N. Go.
Molecular dynamics simulation shows large volume fluctuation of proteins.
Eur. Biophys. J. 2000 29: 472-480
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