# -*- coding: utf-8 -*-
# **************************************************************************
# *
# * Authors:     Mohamad Harastani (mohamad.harastani@upmc.fr)
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307  USA
# *
# *  All comments concerning this program package may be sent to the
# *  e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************

"""

@article{Jin2014,
title = "Iterative Elastic 3D-to-2D Alignment Method Using Normal Modes for Studying Structural Dynamics of Large Macromolecular Complexes",
journal = "Structure",
volume = "22",
pages = "1 - 11",
year = "2014",
doi = "http://dx.doi.org/10.1016/j.str.2014.01.004",
url = "http://www.ncbi.nlm.nih.gov/pubmed/24508340",
author = "Jin, Q. and Sorzano, C. O. S. and de la Rosa-Trevín, J. M. and Bilbao-Castro, J. R. and Núñez-Ramirez, R. and Llorca, O. and Tama, F. and Jonic, S.",
keywords = "Normal mode analysis, NMA "
}

@article{Jonic2005,
title = "Spline-based image-to-volume registration for three-dimensional electron microscopy ",
journal = "Ultramicroscopy ",
volume = "103",
number = "4",
pages = "303 - 317",
year = "2005",
issn = "0304-3991",
doi = "http://dx.doi.org/10.1016/j.ultramic.2005.02.002",
url = "http://www.sciencedirect.com/science/article/pii/S0304399105000173",
author = "Jonic, S. and C.O.S. Sorzano and P. Thevenaz and C. El-Bez and S. De Carlo and M. Unser",
keywords = "2D/3D registration, Splines, 3DEM, Angular assignment "
}

@article{Nogales2013,
title={3DEM Loupe: analysis of macromolecular dynamics using structures from electron microscopy},
author={Nogales-Cadenas, R. and Jonic, S. and Tama, F. and Arteni, A. A. and Tabas-Madrid, D. and V{\'a}zquez, M. and Pascual-Montano, A. and Sorzano, C. O. S.},
journal={Nucleic acids research},
year={2013},
publisher={Oxford Univ Press},
doi={http://dx.doi.org/10.1093/nar/gkt385}
}


@article{Sorzano2004b,
    volume = "146", 
    doi = "http://dx.doi.org/10.1016/j.jsb.2004.01.006", 
    author = "Sorzano, C.O.S. and S. Jonic and C. El-Bez and J.M. Carazo and S. De Carlo and P. Thevenaz and M. Unser", 
    title = "A multiresolution approach to orientation assignment in 3D electron microscopy of single particles ", 
    journal = "JSB ", 
    issn = "1047-8477", 
    number = "3", 
    note = "", 
    link = "http://www.sciencedirect.com/science/article/pii/S1047847704000073", 
    year = "2004", 
    pages = "381 - 392"
}

@article{Sorzano2016,
title = "StructMap: Elastic distance analysis of electron microscopy maps for studying conformational changes",
journal = "Biophysical J.",
volume = "110",
number = "",
pages = "1753-1765",
year = "2016",
note = "",
issn = "",
doi = "http://doi.org/10.1016/j.bpj.2016.03.019",
url = "http://doi.org/10.1016/j.bpj.2016.03.019",
author = "C.O.S. Sorzano, A.L. Álvarez-Cabrera, M. Kazemi, J.M. Carazo, S. Jonic",
keywords = ""
}


@article{harastani2020hybrid,
  title={Hybrid Electron Microscopy Normal Mode Analysis with Scipion},
  author={Harastani, Mohamad and Sorzano, Carlos Oscar S and Joni{\'c}, Slavica},
  journal={Protein Science},
  volume={29},
  number={1},
  pages={223--236},
  year={2020},
  publisher={Wiley Online Library},
  doi= {https://doi.org/10.1002/pro.3772}
}

"""

