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Florence Tama - Publications

Affiliations: 
2006-2012 University of Arizona, Tucson, AZ 
 2013- RIKEN 
 2016- Nagoya University, Nagoya-shi, Aichi-ken, Japan 
Area:
Computational Biophysics, Computational Structural Biology
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71 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
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  0.323
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  0.306
2022 Vuillemot R, Miyashita O, Tama F, Rouiller I, Jonic S. NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynamics atomic displacements. Journal of Molecular Biology. 434: 167483. PMID 35150654 DOI: 10.1016/j.jmb.2022.167483  0.302
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  0.384
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  0.366
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  0.322
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  0.353
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  0.36
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  0.395
2019 Putarjunan A, Ruble J, Srivastava A, Zhao C, Rychel AL, Hofstetter AK, Tang X, Zhu JK, Tama F, Zheng N, Torii KU. Bipartite anchoring of SCREAM enforces stomatal initiation by coupling MAP kinases to SPEECHLESS. Nature Plants. PMID 31235876 DOI: 10.1038/S41477-019-0440-X  0.331
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  0.354
2019 Tama F. Hybrid Modeling Approaches to Study Structures and Dynamics of Biological Systems Biophysical Journal. 116: 331a. DOI: 10.1016/J.Bpj.2018.11.1799  0.33
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  0.388
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  0.346
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  0.384
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  0.36
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  0.382
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  0.319
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  0.355
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  0.317
2017 Srivastava A, Hirota T, Irle S, Tama F. Conformational dynamics of human Protein Kinase CK2α and its effect on function and inhibition. Proteins. PMID 29243286 DOI: 10.1002/Prot.25444  0.38
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  0.36
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  0.405
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  0.336
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  0.437
2014 Sorzano CO, de la Rosa-Trevín JM, Tama F, Jonić S. Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol. Journal of Structural Biology. 188: 134-41. PMID 25268657 DOI: 10.1016/J.Jsb.2014.09.005  0.351
2014 Patel S, Vierling E, Tama F. Replica exchange molecular dynamics simulations provide insight into substrate recognition by small heat shock proteins. Biophysical Journal. 106: 2644-55. PMID 24940782 DOI: 10.1016/J.Bpj.2014.04.048  0.37
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  0.335
2014 Jin Q, Sorzano CO, de la Rosa-Trevín JM, Bilbao-Castro JR, Núñez-Ramírez R, Llorca O, Tama F, Jonić S. Iterative elastic 3D-to-2D alignment method using normal modes for studying structural dynamics of large macromolecular complexes. Structure (London, England : 1993). 22: 496-506. PMID 24508340 DOI: 10.1016/J.Str.2014.01.004  0.437
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  0.342
2014 Jin Q, Carlos Oscar SS, de la Rosa-Trevín JM, Tama F, Jonić S. Macromolecular Dynamics by Hybrid Electron Microscopy Normal Mode Analysis Microscopy and Microanalysis. 20: 1218-1219. DOI: 10.1017/S143192761400782X  0.424
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  0.304
2013 Lyumkis D, Talley H, Stewart A, Shah S, Park CK, Tama F, Potter CS, Carragher B, Horton NC. Allosteric regulation of DNA cleavage and sequence-specificity through run-on oligomerization. Structure (London, England : 1993). 21: 1848-58. PMID 24055317 DOI: 10.1016/J.Str.2013.08.012  0.315
2013 Nogales-Cadenas R, Jonic S, Tama F, Arteni AA, Tabas-Madrid D, Vázquez M, Pascual-Montano A, Sorzano CO. 3DEM Loupe: Analysis of macromolecular dynamics using structures from electron microscopy. Nucleic Acids Research. 41: W363-7. PMID 23671335 DOI: 10.1093/Nar/Gkt385  0.459
2013 Baker JL, Biais N, Tama F. Steered molecular dynamics simulations of a type IV pilus probe initial stages of a force-induced conformational transition. Plos Computational Biology. 9: e1003032. PMID 23592974 DOI: 10.1371/Journal.Pcbi.1003032  0.357
2013 Ahmed A, Tama F. Consensus among multiple approaches as a reliability measure for flexible fitting into cryo-EM data. Journal of Structural Biology. 182: 67-77. PMID 23416197 DOI: 10.1016/J.Jsb.2013.02.002  0.39
2013 Fritz BG, Roberts SA, Ahmed A, Breci L, Li W, Weichsel A, Brailey JL, Wysocki VH, Tama F, Montfort WR. Molecular model of a soluble guanylyl cyclase fragment determined by small-angle X-ray scattering and chemical cross-linking. Biochemistry. 52: 1568-82. PMID 23363317 DOI: 10.1021/Bi301570M  0.335
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  0.356
2012 Zhang X, He X, Baker J, Tama F, Chang G, Wright SH. Twelve transmembrane helices form the functional core of mammalian MATE1 (multidrug and toxin extruder 1) protein. The Journal of Biological Chemistry. 287: 27971-82. PMID 22722930 DOI: 10.1074/Jbc.M112.386979  0.348
2012 Baker J, Wright SH, Tama F. Simulations of substrate transport in the multidrug transporter EmrD. Proteins. 80: 1620-32. PMID 22434745 DOI: 10.1002/Prot.24056  0.318
2012 Baumann BA, Taylor DW, Huang Z, Tama F, Fagnant PM, Trybus KM, Taylor KA. Phosphorylated smooth muscle heavy meromyosin shows an open conformation linked to activation. Journal of Molecular Biology. 415: 274-87. PMID 22079364 DOI: 10.1016/J.Jmb.2011.10.047  0.315
2012 Ahmed A, Whitford PC, Sanbonmatsu KY, Tama F. Consensus among flexible fitting approaches improves the interpretation of cryo-EM data. Journal of Structural Biology. 177: 561-70. PMID 22019767 DOI: 10.1016/J.Jsb.2011.10.002  0.427
2012 Taylor KA, Baumann BA, Taylor DW, Huang Z, Tama F, Fagnant PM, Trybus KM. Phosphorylated Smooth Muscle Heavy Meromyosin Shows an Open Conformation: Implications for the Structure of Myosin with One Head Phosphorylated Biophysical Journal. 102: 159a. DOI: 10.1016/J.Bpj.2011.11.864  0.333
2011 Whitford PC, Ahmed A, Yu Y, Hennelly SP, Tama F, Spahn CM, Onuchic JN, Sanbonmatsu KY. Excited states of ribosome translocation revealed through integrative molecular modeling. Proceedings of the National Academy of Sciences of the United States of America. 108: 18943-8. PMID 22080606 DOI: 10.1073/Pnas.1108363108  0.432
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  0.434
2010 Gorba C, Tama F. Normal Mode Flexible Fitting of High-Resolution Structures of Biological Molecules Toward SAXS Data. Bioinformatics and Biology Insights. 4: 43-54. PMID 20634984 DOI: 10.4137/Bbi.S4551  0.441
2010 Katayama H, Wang J, Tama F, Chollet L, Gogol EP, Collier RJ, Fisher MT. Three-dimensional structure of the anthrax toxin pore inserted into lipid nanodiscs and lipid vesicles. Proceedings of the National Academy of Sciences of the United States of America. 107: 3453-7. PMID 20142512 DOI: 10.1073/Pnas.1000100107  0.367
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  0.463
2008 Orzechowski M, Tama F. Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations. Biophysical Journal. 95: 5692-705. PMID 18849406 DOI: 10.1529/Biophysj.108.139451  0.413
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  0.409
2006 Tama F, Ren G, Brooks CL, Mitra AK. Model of the toxic complex of anthrax: responsive conformational changes in both the lethal factor and the protective antigen heptamer. Protein Science : a Publication of the Protein Society. 15: 2190-200. PMID 16943448 DOI: 10.1110/Ps.062293906  0.52
2006 Sherman MB, Guenther RH, Tama F, Sit TL, Brooks CL, Mikhailov AM, Orlova EV, Baker TS, Lommel SA. Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release. Journal of Virology. 80: 10395-406. PMID 16920821 DOI: 10.1128/Jvi.01137-06  0.487
2006 Tama F, Brooks CL. Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Annual Review of Biophysics and Biomolecular Structure. 35: 115-33. PMID 16689630 DOI: 10.1146/Annurev.Biophys.35.040405.102010  0.539
2006 Konecny R, Trylska J, Tama F, Zhang D, Baker NA, Brooks CL, McCammon JA. Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers. 82: 106-20. PMID 16278831 DOI: 10.1002/Bip.20409  0.472
2006 Mitra K, Schaffitzel C, Shaikh T, Tama F, Jenni S, Brooks CL, Ban N, Frank J. Erratum: Structure of the E. coli protein-conducting channel bound to a translating ribosome Nature. 443: 718-718. DOI: 10.1038/Nature05086  0.465
2005 Mitra K, Schaffitzel C, Shaikh T, Tama F, Jenni S, Brooks CL, Ban N, Frank J. Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature. 438: 318-24. PMID 16292303 DOI: 10.1038/Nature04133  0.521
2005 Falke S, Tama F, Brooks CL, Gogol EP, Fisher MT. The 13 angstroms structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy. Journal of Molecular Biology. 348: 219-30. PMID 15808865 DOI: 10.1016/J.Jmb.2005.02.027  0.568
2005 Tama F, Feig M, Liu J, Brooks CL, Taylor KA. The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function. Journal of Molecular Biology. 345: 837-54. PMID 15588830 DOI: 10.1016/J.Jmb.2004.10.084  0.623
2005 Tama F, Brooks CL. Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis. Journal of Molecular Biology. 345: 299-314. PMID 15571723 DOI: 10.1016/J.Jmb.2004.10.054  0.526
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  0.564
2004 Trylska J, Konecny R, Tama F, Brooks CL, McCammon JA. Ribosome motions modulate electrostatic properties. Biopolymers. 74: 423-31. PMID 15274086 DOI: 10.1002/Bip.20093  0.472
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  0.568
2004 Wriggers W, Chacón P, Kovacs JA, Tama F, Birmanns S. Topology representing neural networks reconcile biomolecular shape, structure, and dynamics Neurocomputing. 56: 365-379. DOI: 10.1016/J.Neucom.2003.09.007  0.376
2003 Tama F, Valle M, Frank J, Brooks CL. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proceedings of the National Academy of Sciences of the United States of America. 100: 9319-23. PMID 12878726 DOI: 10.1073/Pnas.1632476100  0.589
2003 Tama F. Normal mode analysis with simplified models to investigate the global dynamics of biological systems. Protein and Peptide Letters. 10: 119-32. PMID 12678809 DOI: 10.2174/0929866033479077  0.352
2003 Chacón P, Tama F, Wriggers W. Mega-Dalton biomolecular motion captured from electron microscopy reconstructions. Journal of Molecular Biology. 326: 485-92. PMID 12559916 DOI: 10.1016/S0022-2836(02)01426-2  0.388
2002 Tama F, Wriggers W, Brooks CL. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. Journal of Molecular Biology. 321: 297-305. PMID 12144786 DOI: 10.1016/S0022-2836(02)00627-7  0.565
2002 Tama F, Brooks CL. The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. Journal of Molecular Biology. 318: 733-47. PMID 12054819 DOI: 10.1016/S0022-2836(02)00135-3  0.55
2001 Tama F, Sanejouand Y-. Conformational change of proteins arising from normal mode calculations Protein Engineering. 14: 1-6. PMID 11287673 DOI: 10.1093/Protein/14.1.1  0.392
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  0.338
2000 Tama F, Gadea FX, Marques O, Sanejouand YH. Building-block approach for determining low-frequency normal modes of macromolecules Proteins: Structure, Function and Genetics. 41: 1-7. PMID 10944387 DOI: 10.1002/1097-0134(20001001)41:1<1::Aid-Prot10>3.0.Co;2-P  0.349
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