Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

A description is given of new tools to facilitate model building and refinement into electron cryo-microscopy reconstructions.

[1]  D. Baker,et al.  Refinement of protein structures into low-resolution density maps using rosetta. , 2009, Journal of molecular biology.

[2]  S. Scheres,et al.  Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles , 2013, eLife.

[3]  Pablo Chacón,et al.  iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates. , 2013, Journal of structural biology.

[4]  Zhe Wang,et al.  Real-space refinement with DireX: from global fitting to side-chain improvements. , 2012, Biopolymers.

[5]  Wen Jiang,et al.  Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling , 2013, Proceedings of the National Academy of Sciences.

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

[7]  H. Noller,et al.  Structural basis for translation termination on the 70S ribosome , 2008, Nature.

[8]  Anna Marie Pyle,et al.  RCrane: semi-automated RNA model building , 2012, Acta crystallographica. Section D, Biological crystallography.

[9]  A. R. Srinivasan,et al.  Geometric parameters in nucleic acids: Nitrogenous bases , 1996 .

[10]  Gunnar F. Schröder,et al.  Cross-validation in cryo-EM–based structural modeling , 2013, Proceedings of the National Academy of Sciences.

[11]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[12]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[13]  Fei Long,et al.  BALBES: a molecular-replacement pipeline , 2007, Acta crystallographica. Section D, Biological crystallography.

[14]  John E. Johnson,et al.  An automated procedure for detecting protein folds from sub-nanometer resolution electron density. , 2010, Journal of structural biology.

[15]  M. Ueda,et al.  Structure of the carboxypeptidase Y inhibitor IC in complex with the cognate proteinase reveals a novel mode of the proteinase-protein inhibitor interaction. , 2005, Journal of molecular biology.

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

[17]  Garib N. Murshudov,et al.  Conformation-independent structural comparison of macromolecules with ProSMART , 2014, Acta crystallographica. Section D, Biological crystallography.

[18]  Randy J. Read,et al.  Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement , 2012, Acta crystallographica. Section D, Biological crystallography.

[19]  Victor H Hernandez,et al.  Nature Methods , 2007 .

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

[21]  M. Banfield,et al.  The crystal structure of PEBP-2, a homologue of the PEBP/RKIP family. , 2002, Acta crystallographica. Section D, Biological crystallography.

[22]  Anton I. Petrov,et al.  Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas , 2013, RNA.

[23]  Kai Zhang,et al.  Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping , 2011, Proceedings of the National Academy of Sciences.

[24]  D. Agard,et al.  Electron counting and beam-induced motion correction enable near atomic resolution single particle cryoEM , 2013, Nature Methods.

[25]  Liisa Holm,et al.  Dali server: conservation mapping in 3D , 2010, Nucleic Acids Res..

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

[27]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

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

[29]  Paul Emsley,et al.  Handling ligands with Coot , 2012 .

[30]  Ardan Patwardhan,et al.  Collaborative Computational Project for Electron cryo-Microscopy , 2015, Acta crystallographica. Section D, Biological crystallography.

[31]  W. Kühlbrandt,et al.  Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector , 2014, eLife.

[32]  G. McMullan,et al.  Electronic detectors for electron microscopy , 2011, Quarterly Reviews of Biophysics.

[33]  J. Rubinstein,et al.  Beyond blob-ology , 2014, Science.

[34]  S. Scheres.  Beam-induced motion correction for sub-megadalton cryo-EM particles , 2014, eLife.

[35]  Joachim Frank,et al.  An approach to examining model dependence in EM reconstructions using cross-validation. , 2003, Journal of structural biology.

[36]  Wilma K. Olson,et al.  BPS: a database of RNA base-pair structures , 2008, Nucleic Acids Res..

[37]  Alexei Vagin,et al.  Molecular replacement with MOLREP. , 2010, Acta crystallographica. Section D, Biological crystallography.

[38]  David Baker,et al.  Cryo‐EM model validation using independent map reconstructions , 2013, Protein science : a publication of the Protein Society.

[39]  Sjors H W Scheres,et al.  SPI-EM: towards a tool for predicting CATH superfamilies in 3D-EM maps. , 2005, Journal of molecular biology.

[40]  A. Brunger.  Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. , 1992 .

[41]  John D. Westbrook,et al.  EMDataBank.org: unified data resource for CryoEM , 2010, Nucleic Acids Res..

[42]  D. Julius,et al.  Structure of the TRPV1 ion channel determined by electron cryo-microscopy , 2013, Nature.

[43]  V. Luzzati,et al.  Traitement statistique des erreurs dans la determination des structures cristallines , 1952 .

[44]  M. Baker,et al.  Identification of secondary structure elements in intermediate-resolution density maps. , 2007, Structure.

[45]  David A. Lee,et al.  New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures , 2012, Nucleic Acids Res..

[46]  Gert Vriend,et al.  Re-refinement from deposited X-ray data can deliver improved models for most PDB entries , 2009, Acta crystallographica. Section D, Biological crystallography.

[47]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[48]  S. Scheres,et al.  Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine , 2014, eLife.

[49]  Fei Long,et al.  REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. , 2004, Acta crystallographica. Section D, Biological crystallography.

[50]  Koji Yonekura,et al.  Conformational change of flagellin for polymorphic supercoiling of the flagellar filament , 2010, Nature Structural &Molecular Biology.

[51]  K Henrick,et al.  Electronic Reprint Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions , 2022 .

[52]  Potential use of real-space refinement in protein structure determination. , 1997, Acta crystallographica. Section D, Biological crystallography.

[53]  Ilya N. Shindyalov,et al.  PDP: protein domain parser , 2003, Bioinform..

[54]  Eric Westhof,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[55]  Keren Lasker,et al.  Finding the right fit: chiseling structures out of cryo-electron microscopy maps. , 2014, Current opinion in structural biology.

[56]  Hyunjoong Kim,et al.  Functional Analysis I , 2017 .

[57]  Vincent B. Chen,et al.  Correspondence e-mail: , 2000 .

[58]  Matthew L. Baker,et al.  Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps. , 2012, Biopolymers.

[59]  Randy J. Read,et al.  Advancing Methods for Biomolecular Crystallography , 2013 .

[60]  Fei Long,et al.  Low-resolution refinement tools in REFMAC5 , 2012, Acta crystallographica. Section D, Biological crystallography.

[61]  W. Chiu,et al.  Comparison of Segger and other methods for segmentation and rigid-body docking of molecular components in cryo-EM density maps. , 2012, Biopolymers.

[62]  Christoph Leidig,et al.  60S ribosome biogenesis requires rotation of the 5S ribonucleoprotein particle , 2014, Nature Communications.

[63]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[64]  Michael Frankfurter,et al.  Numerical Recipes In C The Art Of Scientific Computing , 2016 .

[65]  V. Luzzati,et al.  Resolution d'un structure cristalline lorsque les positions d'une partie des atoms sont connues: traitement statistique , 1953 .

[66]  Alan Brown,et al.  Structure of the Yeast Mitochondrial Large Ribosomal Subunit , 2014, Science.

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

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

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

[70]  Richard B. Nelson,et al.  Simplified calculation of eigenvector derivatives , 1976 .

[71]  Leonardo G. Trabuco,et al.  Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. , 2008, Structure.

[72]  W. Kühlbrandt.  The Resolution Revolution , 2014, Science.

[73]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .

[74]  P E Bourne,et al.  The Protein Data Bank. , 2002, Nucleic acids research.

[75]  Friedrich Förster,et al.  Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome , 2014, Proceedings of the National Academy of Sciences.

[76]  V. Ramakrishnan,et al.  Initiation of Translation by Cricket Paralysis Virus IRES Requires Its Translocation in the Ribosome , 2014, Cell.

[77]  G. Langlet,et al.  International Tables for Crystallography , 2002 .

[78]  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.