Mitigating local over-fitting during single particle reconstruction with SIDESPLITTER

Graphical abstract

[1]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[2]  M. Baker,et al.  Outcome of the First Electron Microscopy Validation Task Force Meeting , 2012, Structure.

[3]  Jianpeng Ma,et al.  The crystal structure of murine p97/VCP at 3.6A. , 2003, Journal of structural biology.

[4]  R. Handel.  Probability in High Dimension , 2014 .

[5]  Yong Zi Tan,et al.  Structure and Drug Resistance of the Plasmodium falciparum Transporter PfCRT , 2019, Nature.

[6]  N Grigorieff,et al.  Frealign: An Exploratory Tool for Single-Particle Cryo-EM. , 2016, Methods in enzymology.

[7]  Dmitry Lyumkis,et al.  Challenges and opportunities in cryo-EM single-particle analysis , 2019, The Journal of Biological Chemistry.

[8]  A. Steven,et al.  One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions. , 2013, Journal of structural biology.

[9]  Takanori Nakane,et al.  Cryo-EM structure of the human L-type amino acid transporter 1 in complex with glycoprotein CD98hc , 2019, Nature Structural & Molecular Biology.

[10]  R. Bracewell.  Strip Integration in Radio Astronomy , 1956 .

[11]  Guanghui Yang,et al.  Sampling the conformational space of the catalytic subunit of human γ-secretase , 2015, bioRxiv.

[12]  M. Heel,et al.  Exact filters for general geometry three dimensional reconstruction , 1986 .

[13]  Hstau Y Liao,et al.  Definition and estimation of resolution in single-particle reconstructions. , 2010, Structure.

[14]  Martyn Winn,et al.  Recent developments in the CCP-EM software suite , 2017, Acta crystallographica. Section D, Structural biology.

[15]  N. Pannu,et al.  REFMAC5 for the refinement of macromolecular crystal structures , 2011, Acta crystallographica. Section D, Biological crystallography.

[16]  Shaoxia Chen,et al.  Prevention of overfitting in cryo-EM structure determination , 2012, Nature Methods.

[17]  N Grigorieff,et al.  Resolution measurement in structures derived from single particles. , 2000, Acta crystallographica. Section D, Biological crystallography.

[18]  R. Henderson,et al.  Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. , 2003, Journal of molecular biology.

[19]  Dominika Elmlund,et al.  Cryogenic electron microscopy and single-particle analysis. , 2015, Annual review of biochemistry.

[20]  José María Carazo,et al.  MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps. , 2018, Structure.

[21]  J M Carazo,et al.  Advances in image processing for single-particle analysis by electron cryomicroscopy and challenges ahead. , 2018, Current opinion in structural biology.

[22]  R. Henderson,et al.  High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy☆ , 2013, Ultramicroscopy.

[23]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[24]  D. Wigley,et al.  Mechanism for nuclease regulation in RecBCD , 2016, eLife.

[25]  David J. Fleet,et al.  cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination , 2017, Nature Methods.

[26]  N. Grigorieff,et al.  Noise bias in the refinement of structures derived from single particles. , 2004, Ultramicroscopy.

[27]  Garib N Murshudov,et al.  Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM , 2018, Acta crystallographica. Section D, Structural biology.

[28]  J M Carazo,et al.  Three-dimensional reconstruction methods in Single Particle Analysis from transmission electron microscopy data. , 2015, Archives of biochemistry and biophysics.

[29]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[30]  Rafael Ayala,et al.  Structure and dynamics of the yeast SWR1-nucleosome complex , 2018, Science.

[31]  M. van Heel,et al.  Fourier shell correlation threshold criteria. , 2005, Journal of structural biology.

[32]  Sjors H.W. Scheres,et al.  RELION: Implementation of a Bayesian approach to cryo-EM structure determination , 2012, Journal of structural biology.

[33]  J. Frank,et al.  The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles. , 1994, Ultramicroscopy.

[34]  Hemant D. Tagare,et al.  The Local Resolution of Cryo-EM Density Maps , 2013, Nature Methods.

[35]  Steven G. Johnson,et al.  The Design and Implementation of FFTW3 , 2005, Proceedings of the IEEE.

[36]  J. Jensen.  Sur les fonctions convexes et les inégalités entre les valeurs moyennes , 1906 .

[37]  Sjors H.W. Scheres,et al.  A Bayesian View on Cryo-EM Structure Determination , 2012, 2012 9th IEEE International Symposium on Biomedical Imaging (ISBI).

[38]  Joachim Frank,et al.  Advances in the field of single-particle cryo-electron microscopy over the last decade , 2017, Nature Protocols.

[39]  David J. Fleet,et al.  Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction , 2019, Nature Methods.

[40]  Dominika Elmlund,et al.  High-resolution cryo-EM: the nuts and bolts. , 2017, Current opinion in structural biology.

[41]  José María Carazo,et al.  Automatic local resolution-based sharpening of cryo-EM maps , 2018, bioRxiv.

[42]  Kailash Ramlaul,et al.  A Local Agreement Filtering Algorithm for Transmission EM Reconstructions , 2019, Journal of structural biology.

[43]  P. Penczek.  Resolution measures in molecular electron microscopy. , 2010, Methods in enzymology.

[44]  Roberto Marabini,et al.  MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography , 2015, Journal of structural biology.

[45]  Bridget Carragher,et al.  Structure and Drug Resistance of the Plasmodium Falciparum Transporter PfCRT , 2020 .