Abrishami2013
- author = Abrishami V. and Zaldívar-Peraza A. and de la Rosa-Trevín J. M. and Vargas J. and Otón J. and Marabini R. and Shkolnisky Y. and Carazo J. M. and Sorzano C. O. S.
- title = A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
- volume = 29
- number = 19
- pages = 2460-2468
- year = 2013
- doi = http://dx.doi.org/10.1093/bioinformatics/btt429
- url = http://bioinformatics.oxfordjournals.org/content/29/19/2460.abstract
- journal = Bioinformatics
Abrishami2015
- title = Alignment of direct detection device micrographs using a robust Optical Flow approach
- journal = Journal of Structural Biology
- volume = 189
- number = 3
- pages = 163 - 176
- year = 2015
- note =
- issn = 1047-8477
- doi = http://dx.doi.org/10.1016/j.jsb.2015.02.001
- url = http://www.sciencedirect.com/science/article/pii/S1047847715000313
- author = Vahid Abrishami and Javier Vargas and Xueming Li and Yifan Cheng and Roberto Marabini and Carlos Óscar Sánchez Sorzano and José María Carazo
- keywords = Direct detection devices
- keywords = Beam induced motion
- keywords = Single particle analysis
- keywords = Electron microscopy
Chen2013
- title = Fast and accurate reference-free alignment of subtomograms
- journal = Journal of Structural Biology
- volume = 182
- number = 3
- pages = 235 - 245
- year = 2013
- note =
- issn = 1047-8477
- doi = http://dx.doi.org/10.1016/j.jsb.2013.03.002
- url = http://www.sciencedirect.com/science/article/pii/S1047847713000737
- author = Yuxiang Chen and Stefan Pfeffer and Thomas Hrabe and Jan Michael Schuller and Friedrich Förster
- keywords = Cryo-electron tomography
- keywords = Subtomogram averaging
- keywords = Spherical harmonics
Cherian2013
- title = Jensen-Bregman LogDet divergence with application to efficient similarity search for covariance matrices
- journal = IEEE Trans Pattern Anal Mach Intell
- volume = 35
- pages = 2161-2174
- year = 2013
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- author = Cherian A. and Sra S. and Banerjee A. and Papanikolopoulos N.
delaRosaTrevin2013
- title = Xmipp 3.0: An improved software suite for image processing in electron microscopy
- journal = JSB
- volume = 184
- number = 2
- pages = 321 - 328
- year = 2013
- issn = 1047-8477
- doi = http://dx.doi.org/10.1016/j.jsb.2013.09.015
- url = http://www.sciencedirect.com/science/article/pii/S1047847713002566
- author = de la Rosa-Trevín J.M. and Oton J. and R. Marabini and A. Zaldívar and J. Vargas and J.M. Carazo and Sorzano C.O.S.
- keywords = Electron microscopy Single particles analysis Image processing Software package
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
Jonic2005
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\'azquez 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
Otsu1979
- title = A Threshold Selection Method from Gray-Level Histograms
- journal = Systems Man and Cybernetics IEEE Transactions
- volume = 9
- number = 2
- pages = 62 - 66
- year = 1979
- issn = 0018-9472
- doi = http://dx.doi.org/10.1109/TSMC.1979.4310076
- author = Otsu N.
Pascual2000
- title = Mapping and fuzzy classification of macromolecular images using self-organizing neural networks
- journal = Ultramicroscopy
- volume = 84
- number = 1-2
- pages = 85 - 99
- year = 2000
- note =
- issn = 0304-3991
- doi = http://dx.doi.org/10.1016/S0304-3991(00)00022-X
- url = http://www.sciencedirect.com/science/article/pii/S030439910000022X
- author = Pascual-Montano A and Montserrat Bárcena and J.J Merelo and José-María Carazo
- keywords = Image processing Cluster analysis Neural networks Self-organizing maps Fuzzy logic
PascualMontano2001
- title = A Novel Neural Network Technique for Analysis and Classification of \\EM\\ Single-Particle Images
- journal = JSB
- volume = 133
- number = 2 - 3
- pages = 233 - 245
- year = 2001
- issn = 1047-8477
- doi = http://dx.doi.org/10.1006/jsbi.2001.4369
- url = http://www.sciencedirect.com/science/article/pii/S1047847701943692
- author = Pascual-Montano A and L.E Donate and M Valle and M Bárcena and R.D Pascual-Marqui and J.M Carazo
- keywords = classification cryo-EM image processing neural networks self-organizing maps probability density function kernel functions
PascualMontano2002
- title = Quantitative self-organizing maps for clustering electron tomograms
- journal = JSB
- volume = 138
- number = 1-2
- pages = 114 - 122
- year = 2002
- note =
- issn = 1047-8477
- doi = http://dx.doi.org/10.1016/S1047-8477(02)00008-4
- url = http://www.sciencedirect.com/science/article/pii/S1047847702000084
- author = Pascual-Montano A and K.A. Taylor and H. Winkler and R.D. Pascual-Marqui and J.-M. Carazo
- keywords = Classification Electron tomography Image processing Neural networks Self-organizing maps Probability density function Kernel functions Actin Myosin Muscle proteins
Rosenthal2003
Scheres2005a
- title = Maximum-likelihood Multi-reference Refinement for Electron Microscopy Images
Journal=J. Mol. Biol.
- volume = 348
- number = 1
- pages = 139 - 149
- year = 2005
- issn = 0022-2836
- doi = http://dx.doi.org/10.1016/j.jmb.2005.02.031
- url = http://www.sciencedirect.com/science/article/pii/S0022283605001932
- author = Scheres Sjors H.W. and Valle Mikel and Rafael Núñez and Carlos O.S. Sorzano and Roberto Marabini and Gabor T. Herman and Jose-Maria Carazo
- keywords = maximum-likelihood multi-reference refinement single-particles 2D-alignment classification
Scheres2005b
- author = Scheres Sjors H.W. and Valle Mikel and Carazo José-María
- title = Fast maximum-likelihood refinement of electron microscopy images.
- journal = Bioinformatics
- year = 2005
- volume = 21 Suppl 2
- pages = ii243--ii244
- month = Sep
- doi = http://dx.doi.org/10.1093/bioinformatics/bti1140
- url = http://dx.doi.org/10.1093/bioinformatics/bti1140
- keywords = Algorithms; Cryoelectron Microscopy methods; Image Enhancement methods;
Image Interpretation Computer-Assisted methods; Imaging Three-Dimensional
methods; Likelihood Functions; Reproducibility of Results; Sensitivity
and Specificity
Scheres2007a
- author = Scheres Sjors H. W. and Haixiao Gao and Mikel Valle and Gabor T Herman
- and Paul P B Eggermont and et.al.
- title = Disentangling conformational states of macromolecules in 3D-EM through
- likelihood optimization.
- journal = Nature Methods
- year = 2007
- volume = 4
- pages = 27--29
- number = 1
- month = Jan
- doi = http://dx.doi.org/10.1038/nmeth992
- keywords = Antigens Polyomavirus Transforming; Escherichia coli; Image Processing
Computer-Assisted; Imaging Three-Dimensional; Likelihood Functions;
Microscopy Electron; Models Molecular; Protein Conformation; Ribosomes;
Sensitivity and Specificity; Simian virus 40
Scheres2007b
- author = Scheres Sjors H. W. and Núñez-Ramírez Rafael and Gómez-Llorente
- Yacob and San Martín Carmen and Eggermont Paul P B. and Carazo
- José María
- title = Modeling experimental image formation for likelihood-based classification
- of electron microscopy data.
- journal = Structure
- year = 2007
- volume = 15
- pages = 1167--1177
- number = 10
- month = Oct
- doi = http://dx.doi.org/10.1016/j.str.2007.09.003
- url = http://dx.doi.org/10.1016/j.str.2007.09.003
- keywords = Algorithms; Antigens Polyomavirus Transforming chemistry/ultrastructure;
Archaeal Proteins chemistry/ultrastructure; Cryoelectron Microscopy
methods/statistics /&/ numerical data; DNA Helicases chemistry/ultrastructure;
Escherichia coli metabolism; Imaging Three-Dimensional; Likelihood
Functions; Models Molecular; Models Statistical; Protein Conformation;
Ribosomes chemistry/ultrastructure
Scheres2009b
- author = Scheres Sjors H W. and Carazo José María
- title = Introducing robustness to maximum-likelihood refinement of electron-microscopy
- data.
- journal = Acta Crystallogr D Biol Crystallogr
- year = 2009
- volume = 65
- pages = 672--678
- number = Pt 7
- month = Jul
- doi = http://dx.doi.org/10.1107/S0907444909012049
- url = http://dx.doi.org/10.1107/S0907444909012049
- keywords = Algorithms; Cryoelectron Microscopy; Escherichia coli chemistry;
Likelihood Functions; Models Molecular; Peptide Elongation Factor
G chemistry/ultrastructure; Protein Structure Tertiary
Scheres2009c
- author = Scheres Sjors H W. and Melero Roberto and Valle Mikel and Carazo José María
- title = Averaging of Electron Subtomograms and Random Conical Tilt Reconstructions through Likelihood Optimization
- journal = Structure
- year = 2009
- volume = 17
- pages = 1563--1572
- number = 12
- month = Dec
- doi = http://dx.doi.org/10.1016/j.str.2009.10.009
Sorzano2004b
- title = A multiresolution approach to orientation assignment in 3D electron microscopy of single particles
- journal = JSB
- volume = 146
- number = 3
- pages = 381 - 392
- year = 2004
- note =
- issn = 1047-8477
- doi = http://dx.doi.org/10.1016/j.jsb.2004.01.006
- url = http://www.sciencedirect.com/science/article/pii/S1047847704000073
- 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
Sorzano2007a
- Title = Fast robust and accurate determination of transmission electron microscopy contrast transfer function
- Author = Sorzano C. O. S. and Jonic S. and N\'u\\~nez-Ram\'irez R. and Boisset N. and Carazo J. M.
- Journal = J. Structural Biology
- Year = 2007
- Pages = 249--262
- Volume = 160
- doi = http://dx.doi.org/10.1016/j.jsb.2007.08.013
- url = http://www.sciencedirect.com/science/article/pii/S104784770700202X
Sorzano2009d
- title = Effects of the downsampling scheme on three-dimensional electron microscopy of single particles
- journal = Proc. of IEEE Workshop on Intelligent Signal Processing
- pages = 175-179
- year = 2009
- note =
- issn = 978-1-4244-5059-6
- doi = http://dx.doi.org/10.1109/WISP.2009.5286563
- url = http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=5286563
- author = Sorzano C. O. S. and Iriarte-Ruiz A. and Marabini R. and Carazo J. M.
- keywords = Downsampling Single Particles Electron microscopy
Sorzano2010a
- title = A clustering approach to multireference alignment of single-particle projections in electron microscopy
- journal = Journal of Structural Biology
- volume = 171
- number = 2
- pages = 197 - 206
- year = 2010
- note =
- issn = 1047-8477
- doi = http://dx.doi.org/10.1016/j.jsb.2010.03.011
- url = http://www.sciencedirect.com/science/article/pii/S1047847710000882
- author = C.O.S. Sorzano and J.R. Bilbao-Castro and Y. Shkolnisky and M. Alcorlo and R. Melero and G. Caffarena-Fernández and M. Li and G. Xu and R. Marabini and J.M. Carazo
- keywords = Single-particle analysis 2D analysis Multireference analysis Electron microscopy
Sorzano2013
- title = Semiautomatic High-Throughput High-Resolution Protocol for Three-Dimensional Reconstruction of Single Particles in Electron Microscopy
- booktitle = Nanoimaging
- year = 2013
- isbn = 978-1-62703-136-3
- volume = 950
- journal = Methods in Molecular Biology
- editor = Sousa Alioscka A. and Kruhlak Michael J.
- doi = http://dx.doi.org/10.1007/978-1-62703-137-0_11
- publisher = Humana Press
- keywords = Single particle analysis; Electron microscopy; Image processing; 3D reconstruction; Workflows
- author = Sorzano C.O.S. and de la Rosa-Trevín J.M. and Otón J. and Vega J.J. and Cuenca J. and Zaldívar-Peraza A. and Gómez-Blanco J. and Vargas J. and Quintana A. and Marabini Roberto and Carazo José María
- pages = 171-193
Sorzano2014
- title = Outlier detection for single particle analysis in Electron Microscopy
- author = Sorzano C. O. S. and Vargas J. and de la Rosa-Trevín J. M. and Zaldívar-Peraza A. and Otón J. and Abrishami V. and Foche I. and Marabini R. and Caffarena G. and Carazo J. M.
- journal = Proc. Intl. Work-Conference on Bioinformatics and Biomedical Engineering IWBBIO
- year = 2014
- pages = 950
- doi = http://biocomp.cnb.csic.es/~coss/Articulos/Sorzano2014.pdf
Sorzano2015
- author = Sorzano C. O. S. and Vargas J. and de la Rosa-Trevin J. M. and Oton J. and Alvarez-Cabrera A. L. and Abrishami V. and Sesmero E. and Marabini R. and Carazo J. M.
- title = A Statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy
- journal = J. Structural Biology
- year = 2015
- volume = 189
- pages = 213-219
- doi = http://dx.doi.org/10.1016/j.jsb.2015.01.009
Vargas2013a
- author = Vargas J. and Otón J. and Marabini R. and Jonic S. and de la
Rosa-Trevín J. M. and et.al.
- title = FASTDEF: Fast defocus and astigmatism estimation for high-throughput
transmission electron microscopy.
- journal = J. Structural Biology
- doi = http://dx.doi.org/10.1016/j.jsb.2012.12.006
- year = 2013
- volume = 181
- pages = 136--148
- number = 2
- month = Feb
Vargas2013b
- title = Particle quality assessment and sorting for automatic and semiautomatic particle-picking techniques
- journal = J. Structural Biology
- volume = 183
- number = 3
- pages = 342 - 353
- year = 2013
- note =
- issn = 1047-8477
- doi = http://dx.doi.org/10.1016/j.jsb.2013.07.015
- url = http://www.sciencedirect.com/science/article/pii/S1047847713001950
- author = J. Vargas and V. Abrishami and R. Marabini and J.M. de la Rosa-Trevín and A. Zaldivar and J.M. Carazo and C.O.S. Sorzano
- keywords = Electron microscopy Particle picking Machine learning Single particle analysis
Vargas2014
- author = Vargas Javier and Álvarez-Cabrera Ana-Lucia and Marabini Roberto and Carazo Jose M. and Sorzano C. O. S.
- title = Efficient initial volume determination from electron microscopy images of single particles
- volume = 30
- number = 20
- pages = 2891-2898
- year = 2014
- doi = http://dx.doi.org/10.1093/bioinformatics/btu404
- abstract =Motivation: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. The reconstruction process leading to the final 3D map requires an approximate initial model. Generation of an initial model is still an open and challenging problem in single-particle analysis.Results: We present a fast and efficient approach to obtain a reliable low-resolution estimation of the 3D structure of a macromolecule without any a priori knowledge addressing the well-known issue of initial volume estimation in the field of single-particle analysis. The input of the algorithm is a set of class average images obtained from individual projections of a biological object at random and unknown orientations by transmission electron microscopy micrographs. The proposed method is based on an initial non-lineal dimensionality reduction approach which allows to automatically selecting representative small sets of class average images capturing the most of the structural information of the particle under study. These reduced sets are then used to generate volumes from random orientation assignments. The best volume is determined from these guesses using a random sample consensus (RANSAC) approach. We have tested our proposed algorithm which we will term 3D-RANSAC with simulated and experimental data obtaining satisfactory results under the low signal-to-noise conditions typical of cryo-electron microscopy.Availability: The algorithm is freely available as part of the Xmipp 3.1 package [http://xmipp.cnb.csic.es].Contact: [email protected] information: Supplementary data are available at Bioinformatics online.
- URL = http://bioinformatics.oxfordjournals.org/content/30/20/2891.abstract
- eprint = http://bioinformatics.oxfordjournals.org/content/30/20/2891.full.pdf+html
- journal = Bioinformatics
Vilas2016
- title = Fast and automatic identification of particle tilt pairs based on Delaunay triangulation.
- author = Vilas J. L. and Navas J. and Gomez-Blanco J. and de la Rosa-Trevin J. M. and Melero and Peschiera I. and Ferlenghi. I and Cuenca J. and Marabini R. and Carazo J. M. and Vargas J. and Sorzano C. O. S.
- journal = Journal of Structural Biology
- year = 2016
- pages = 525-533
- volume = 196
- doi = http://dx.doi.org/10.1016/j.jsb.2016.10.007
- url = http://www.sciencedirect.com/science/article/pii/S104784771630212X
zhao2013
- author = Zhao Zhizhen and Singer Amit
- title = Fourier-Bessel rotational invariant eigenimages
- volume = 30
- number = 5
- pages = 871--877
- year = 2013
- doi = http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711886/pdf/nihms484949.pdf
- abstract =
- url = http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711886
- eprint = http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711886/pdf/nihms484949.pdf
- journal = Journal of the Optical Society of America. A Optics image science and vision
ponce2011
- author = Ponce Colin and Singer Amit
- title = Computing Steerable Principal Components of a Large Set of Images and Their Rotations
- volume = 20
- number = 11
- pages = 3051--3062
- year = 2011
- doi = http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3719433/pdf/nihms485040.pdf
- abstract =
- url = http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3719433
- eprint = http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3719433/pdf/nihms485040.pdf
- journal = IEEE Trans Image Process
Radermacher1987
- author = Radermacher M. and Wagenknecht T. and Frank J.
- title = Three-dimensional reconstruction from a single-exposure random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli.
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- year = 1987
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- url = http://www.ncbi.nlm.nih.gov/pubmed/3302267
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- journal = Journal of Microscopy
Vargas2014a
- title = Particle alignment reliability in single particle electron cryomicroscopy: a general approach
- journal = Scientific reports
- volume =
- number =
- pages =
- year = 2014
- note =
- issn =
- doi = http://dx.doi.org/10.1038/srep21626
- url = http://dx.doi.org/10.1038/srep21626
- author = Vargas
- keywords = Validation
Marabini2014a
- title = CTF Challenge: Result summary
- journal = J. Structural Biology
- volume =
- number =
- pages =
- year = 2015
- note =
- issn =
- doi = http://doi.org/10.1016/j.jsb.2015.04.003
- url = http://doi.org/10.1016/j.jsb.2015.04.003
- author = Marabini
- keywords = Contrast transfer function
B.Heymann2015
- title = Validation of 3D of 3DEM Reconstructions: The phantom in the noise
- journal = AIMS Biophys
- volume = 2
- number = 1
- pages = 21-35
- year = 2015
- note =
- issn =
- doi = 10.3934/biophy.2015.1.21
- url = http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4440490/
- author = B. Heymann
- keywords =
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 =
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- 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 =
Sorzano2015b
- title = Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revisited.
- author = Sorzano C O S. and Alcorlo M. and de la Rosa-Trevín J. M. and Melero R. and Foche I. and Zaldívar-Peraza A. and del Cano L. and Vargas J. and Abrishami V. and Otón J. and Marabini R. and Carazo J. M.
- journal = Scientific Reports
- year = 2015
- pages = 14290
- volume = 5
- doi = http://dx.doi.org/10.1038/srep14290
- url = http://dx.doi.org/10.1038/srep14290
Vilas2018
- title = MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps
- author = Vilas J. L. and et al
- year = 2018
- journal = Structure
- pages = 337--344
- volume = 26
- doi = 10.1016/j.str.2017.12.018
- url = http://doi.org/10.1016/j.str.2017.12.018
strelak2020flexalign
- AUTHOR = Střelák David and Filipovič Jiří and Jiménez-Moreno Amaya and Carazo Jose María and Sánchez Sorzano Carlos Óscar
- TITLE = FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy
- JOURNAL = Electronics
- VOLUME = 9
- YEAR = 2020
- NUMBER = 6
- ARTICLE-NUMBER = 1040
- URL = http://www.mdpi.com/2079-9292/9/6/1040
- ISSN = 2079-9292
- DOI = http://doi.org/10.3390/electronics9061040
Vilas2023
- AUTHOR = Vilas JL and Tagare HD
- TITLE = A simple and intuitive measurement of directional resolution anisotropy of cryoEM maps
- JOURNAL = Nature Methods
- VOLUME = X
- YEAR = 2023
- NUMBER = X
- ARTICLE-NUMBER = in press
- URL = https://github.com/I2PC/xmipp/wiki/FSO---Fourier-Shell-Occupancy
Fernandez-Gimenez2021
- title = Cryo-EM density maps adjustment for subtraction consensus and sharpening
- journal = Journal of Structural Biology
- volume = 213
- number = 4
- year = 2021
- issn = 1047-8477
- doi = https://doi.org/10.1016/j.jsb.2021.107780
- url = https://www.sciencedirect.com/science/article/pii/S104784772100085X
- author = E. Fernández-Giménez and M. Martínez and R. Sánchez-García and R. Marabini and E. Ramírez-Aportela and
P. Conesa and J.M. Carazo and C.O.S. Sorzano
Strelak2021
- AUTHOR = Strelak David and Jiménez-Moreno Amaya and Vilas José L. and Ramírez-Aportela Erney and Sánchez-García Ruben and Maluenda David and Vargas Javier and Herreros David and Fernández-Giménez Estrella and de Isidro-Gómez Federico P. and Horacek Jan and Myska David and Horacek Martin and Conesa Pablo and Fonseca-Reyna Yunior C. and Jiménez Jorge and Martínez Marta and Harastani Mohamad and Jonić Slavica and Filipovic Jiri and Marabini Roberto and Carazo José M. and Sorzano Carlos O. S.
- TITLE = Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion
- JOURNAL = Molecules
- VOLUME = 26
- YEAR = 2021
- NUMBER = 20
- ARTICLE-NUMBER = 6224
- URL = https://www.mdpi.com/1420-3049/26/20/6224
- PubMedID = 34684805
- ISSN = 1420-3049
- DOI = https://doi.org/10.3390/molecules26206224