Analyses of subnanometer resolution cryo-EM density maps.

[1]  R. Henderson,et al.  Three-dimensional model of purple membrane obtained by electron microscopy , 1975, Nature.

[2]  D. Lipman,et al.  Rapid and sensitive protein similarity searches. , 1985, Science.

[3]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[4]  R. Henderson,et al.  Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. , 1990, Journal of molecular biology.

[5]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[6]  K. Mizuguchi,et al.  Comparison of spatial arrangements of secondary structural elements in proteins. , 1995, Protein engineering.

[7]  M. Karplus,et al.  Evaluation of comparative protein modeling by MODELLER , 1995, Proteins.

[8]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[9]  Akinori Kidera,et al.  Surface of bacteriorhodopsin revealed by high-resolution electron crystallography , 1997, Nature.

[10]  P. Wingfield,et al.  Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy , 1997, Nature.

[11]  G. Kleywegt,et al.  Detecting folding motifs and similarities in protein structures. , 1997, Methods in enzymology.

[12]  B. Böttcher,et al.  Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy , 1997, Nature.

[13]  A. Leslie,et al.  The crystal structure of the human hepatitis B virus capsid. , 1999, Molecular cell.

[14]  J. Mccammon,et al.  Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. , 1999, Journal of structural biology.

[15]  W Chiu,et al.  EMAN: semiautomated software for high-resolution single-particle reconstructions. , 1999, Journal of structural biology.

[16]  N. Volkmann,et al.  Quantitative fitting of atomic models into observed densities derived by electron microscopy. , 1999, Journal of structural biology.

[17]  W. Baumeister,et al.  Macromolecular electron microscopy in the era of structural genomics. , 2000, Trends in biochemical sciences.

[18]  Liam J. McGuffin,et al.  The PSIPRED protein structure prediction server , 2000, Bioinform..

[19]  M. Rossmann,et al.  Fitting atomic models into electron-microscopy maps. , 2000, Acta crystallographica. Section D, Biological crystallography.

[20]  A. Roseman.  Docking structures of domains into maps from cryo-electron microscopy using local correlation. , 2000, Acta crystallographica. Section D, Biological crystallography.

[21]  T L Blundell,et al.  FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. , 2001, Journal of molecular biology.

[22]  M. Baker,et al.  Bridging the information gap: computational tools for intermediate resolution structure interpretation. , 2001, Journal of molecular biology.

[23]  M J Sternberg,et al.  Enhancement of protein modeling by human intervention in applying the automatic programs 3D‐JIGSAW and 3D‐PSSM , 2001, Proteins.

[24]  Matthew L. Baker,et al.  Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus , 2001, Nature Structural Biology.

[25]  Niels Volkmann,et al.  A novel three-dimensional variant of the watershed transform for segmentation of electron density maps. , 2002, Journal of structural biology.

[26]  Pierre Baldi,et al.  Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles , 2002, Proteins.

[27]  J. Frank.  Single-particle imaging of macromolecules by cryo-electron microscopy. , 2002, Annual review of biophysics and biomolecular structure.

[28]  Yasuo Watanabe,et al.  The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins. , 2003, Structure.

[29]  Jianpeng Ma,et al.  A structural-informatics approach for mining beta-sheets: locating sheets in intermediate-resolution density maps. , 2003, Journal of molecular biology.

[30]  F. Quiocho,et al.  Architecture of the herpes simplex virus major capsid protein derived from structural bioinformatics. , 2003, Journal of molecular biology.

[31]  Arne Elofsson,et al.  3D-Jury: A Simple Approach to Improve Protein Structure Predictions , 2003, Bioinform..

[32]  Masafumi Yohda,et al.  Crystal structures of the group II chaperonin from Thermococcus strain KS-1: steric hindrance by the substituted amino acid, and inter-subunit rearrangement between two crystal forms. , 2004, Journal of molecular biology.

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

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

[35]  F. Tama,et al.  Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. , 2004, Journal of structural biology.

[36]  Jianpeng Ma,et al.  A Structural-informatics approach for tracing beta-sheets: building pseudo-C(alpha) traces for beta-strands in intermediate-resolution density maps. , 2004, Journal of molecular biology.

[37]  M. Baker,et al.  Electron cryomicroscopy of biological machines at subnanometer resolution. , 2005, Structure.

[38]  M. Baker,et al.  Common Ancestry of Herpesviruses and Tailed DNA Bacteriophages , 2005, Journal of Virology.

[39]  M. Baker,et al.  Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. , 2005, Journal of structural biology.

[40]  Wah Chiu,et al.  Structure of Ca2+ release channel at 14 A resolution. , 2005, Journal of molecular biology.

[41]  Wah Chiu,et al.  The pore structure of the closed RyR1 channel. , 2005, Structure.

[42]  S. Harrison,et al.  Lipid–protein interactions in double-layered two-dimensional AQP0 crystals , 2005, Nature.

[43]  Wei Zhang,et al.  Combining X-Ray Crystallography and Electron Microscopy , 2005, Structure.

[44]  David E. Kim,et al.  Free modeling with Rosetta in CASP6 , 2005, Proteins.

[45]  Matthew L. Baker,et al.  Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density , 2006, PLoS Comput. Biol..

[46]  Zeyun Yu,et al.  Automated segmentation of molecular subunits in electron cryomicroscopy density maps. , 2006, Journal of structural biology.

[47]  Pierre Tufféry,et al.  SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace , 2006, Nucleic Acids Res..

[48]  Torsten Schwede,et al.  BIOINFORMATICS Bioinformatics Advance Access published November 12, 2005 The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling , 2022 .

[49]  M. Baker,et al.  Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. , 2006, Journal of molecular biology.

[50]  Karsten Suhre,et al.  NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps. , 2006, Acta crystallographica. Section D, Biological crystallography.

[51]  Matthew L. Baker,et al.  Computing a family of skeletons of volumetric models for shape description , 2007, Comput. Aided Des..

[52]  Wen Jiang,et al.  EMAN2: an extensible image processing suite for electron microscopy. , 2007, Journal of structural biology.

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

[54]  Michael Levitt,et al.  Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. , 2007, Structure.

[55]  S. Harrison,et al.  Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction , 2008, Proceedings of the National Academy of Sciences.

[56]  J. J. Fernández,et al.  Sharpening high resolution information in single particle electron cryomicroscopy. , 2008, Journal of structural biology.

[57]  Matthew L. Baker,et al.  Backbone structure of the infectious ε15 virus capsid revealed by electron cryomicroscopy , 2008, Nature.

[58]  Wah Chiu,et al.  Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT , 2008, Nature Structural &Molecular Biology.

[59]  Matthew L. Baker,et al.  Shape modeling and matching in identifying 3D protein structures , 2008, Comput. Aided Des..

[60]  Mirabela Rusu,et al.  Biomolecular pleiomorphism probed by spatial interpolation of coarse models , 2008, Bioinform..

[61]  M. Baker,et al.  Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel , 2008, Proceedings of the National Academy of Sciences.

[62]  Dong-Hua Chen,et al.  De novo backbone trace of GroEL from single particle electron cryomicroscopy. , 2008, Structure.

[63]  Matthew L. Baker,et al.  Rotavirus Architecture at Subnanometer Resolution , 2008, Journal of Virology.

[64]  Ben M. Webb,et al.  Protein structure fitting and refinement guided by cryo-EM density. , 2008, Structure.

[65]  Stephen C Harvey,et al.  YUP.SCX: coaxing atomic models into medium resolution electron density maps. , 2008, Journal of structural biology.

[66]  Christian Cole,et al.  The Jpred 3 secondary structure prediction server , 2008, Nucleic Acids Res..

[67]  Z. Zhou,et al.  3.88 Å structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy , 2008, Nature.

[68]  Niels Volkmann,et al.  Confidence intervals for fitting of atomic models into low-resolution densities , 2009, Acta crystallographica. Section D, Biological crystallography.

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

[70]  M. Sternberg,et al.  Protein structure prediction on the Web: a case study using the Phyre server , 2009, Nature Protocols.

[71]  Leonardo G. Trabuco,et al.  Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography. , 2009, Methods.

[72]  Jorge Navaza,et al.  UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions , 2009, Acta crystallographica. Section D, Biological crystallography.

[73]  Thomas D. Goddard,et al.  Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. , 2010, Journal of structural biology.

[74]  M. Levitt,et al.  Mechanism of Folding Chamber Closure in a Group II Chaperonin , 2010, Nature.

[75]  Wah Chiu,et al.  4.0-Å resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement , 2010, Proceedings of the National Academy of Sciences.

[76]  Yao Cong,et al.  Single particle analysis at high resolution. , 2010, Methods in enzymology.

[77]  B. Honig,et al.  Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement. , 2010, Journal of molecular biology.