Published in Structure on January 01, 2007
Outcome of the first electron microscopy validation task force meeting. Structure (2012) 4.35
EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res (2010) 3.32
Refinement of protein structures into low-resolution density maps using rosetta. J Mol Biol (2009) 2.94
Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. Nat Struct Mol Biol (2010) 2.12
Towards atomic resolution structural determination by single-particle cryo-electron microscopy. Curr Opin Struct Biol (2008) 2.05
Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. J Struct Biol (2007) 1.90
Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions. Acta Crystallogr D Biol Crystallogr (2015) 1.89
4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus. EMBO J (2011) 1.77
Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel. Proc Natl Acad Sci U S A (2008) 1.68
JADAS: a customizable automated data acquisition system and its application to ice-embedded single particles. J Struct Biol (2008) 1.62
Single-particle reconstruction of biological macromolecules in electron microscopy--30 years. Q Rev Biophys (2009) 1.61
Cryo-EM of macromolecular assemblies at near-atomic resolution. Nat Protoc (2010) 1.58
phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. J Struct Funct Genomics (2012) 1.53
Rotavirus architecture at subnanometer resolution. J Virol (2008) 1.48
A test-bed for optimizing high-resolution single particle reconstructions. J Struct Biol (2008) 1.41
EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps. Structure (2009) 1.32
Modeling protein structure at near atomic resolutions with Gorgon. J Struct Biol (2011) 1.29
Resolution measures in molecular electron microscopy. Methods Enzymol (2010) 1.25
Flexible architecture of IP3R1 by Cryo-EM. Structure (2011) 1.24
Single particle cryo-electron microscopy and 3-D reconstruction of viruses. Methods Mol Biol (2014) 1.23
Visualizing GroEL/ES in the act of encapsulating a folding protein. Cell (2013) 1.16
EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps. Structure (2012) 1.15
Hybrid approaches: applying computational methods in cryo-electron microscopy. Curr Opin Struct Biol (2009) 1.11
Structural mechanism of SDS-induced enzyme activity of scorpion hemocyanin revealed by electron cryomicroscopy. Structure (2009) 1.10
Evolutionary bidirectional expansion for the tracing of alpha helices in cryo-electron microscopy reconstructions. J Struct Biol (2011) 1.07
Computing a family of skeletons of volumetric models for shape description. Comput Aided Des (2007) 1.03
Macromolecular structure modeling from 3D EM using VolRover 2.0. Biopolymers (2012) 0.99
Achievable resolution from images of biological specimens acquired from a 4k x 4k CCD camera in a 300-kV electron cryomicroscope. J Struct Biol (2008) 0.98
Near-atomic-resolution cryo-EM for molecular virology. Curr Opin Virol (2011) 0.97
The T=1 capsid protein of Penicillium chrysogenum virus is formed by a repeated helix-rich core indicative of gene duplication. J Virol (2010) 0.96
Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps. Biopolymers (2012) 0.96
Model-building strategies for low-resolution X-ray crystallographic data. Acta Crystallogr D Biol Crystallogr (2009) 0.96
Analyses of subnanometer resolution cryo-EM density maps. Methods Enzymol (2010) 0.95
A structural model of the pore-forming region of the skeletal muscle ryanodine receptor (RyR1). PLoS Comput Biol (2009) 0.94
Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography. Adv Exp Med Biol (2012) 0.93
Constructing and validating initial Cα models from subnanometer resolution density maps with pathwalking. Structure (2012) 0.92
MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures. Bioinformatics (2010) 0.90
Computational methods for constructing protein structure models from 3D electron microscopy maps. J Struct Biol (2013) 0.87
Rapid model building of alpha-helices in electron-density maps. Acta Crystallogr D Biol Crystallogr (2010) 0.87
Architecture of fully occupied GluA2 AMPA receptor-TARP complex elucidated by cryo-EM. Nature (2016) 0.87
Three dimensional shape comparison of flexible proteins using the local-diameter descriptor. BMC Struct Biol (2009) 0.86
A newly isolated reovirus has the simplest genomic and structural organization of any reovirus. J Virol (2014) 0.85
IDSS: deformation invariant signatures for molecular shape comparison. BMC Bioinformatics (2009) 0.84
Structure prediction for the helical skeletons detected from the low resolution protein density map. BMC Bioinformatics (2010) 0.84
The mechanism of vault opening from the high resolution structure of the N-terminal repeats of MVP. EMBO J (2009) 0.83
Epitope insertion at the N-terminal molecular switch of the rabbit hemorrhagic disease virus T = 3 capsid protein leads to larger T = 4 capsids. J Virol (2012) 0.83
Protruding knob-like proteins violate local symmetries in an icosahedral marine virus. Nat Commun (2014) 0.82
Structural studies of large nucleoprotein particles, vaults. Proc Jpn Acad Ser B Phys Biol Sci (2012) 0.82
Interpretation of very low resolution X-ray electron-density maps using core objects. Acta Crystallogr D Biol Crystallogr (2009) 0.82
Improved cryoEM-Guided Iterative Molecular Dynamics--Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction. J Chem Theory Comput (2015) 0.81
An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images. IEEE/ACM Trans Comput Biol Bioinform (2016) 0.80
Unified data resource for cryo-EM. Methods Enzymol (2010) 0.79
Semi-isometric registration of line features for flexible fitting of protein structures. Comput Graph Forum (2010) 0.79
Numerical geometry of map and model assessment. J Struct Biol (2015) 0.78
Estimating loop length from CryoEM images at medium resolutions. BMC Struct Biol (2013) 0.78
Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures. BMC Bioinformatics (2009) 0.77
Comparison of an Atomic Model and Its Cryo-EM Image at the Central Axis of a Helix. Proceedings (IEEE Int Conf Bioinformatics Biomed) (2015) 0.77
Structure and mechanism of the ATP synthase membrane motor inferred from quantitative integrative modeling. J Gen Physiol (2016) 0.77
Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix. J Comput Biol (2016) 0.77
Rapid model building of beta-sheets in electron-density maps. Acta Crystallogr D Biol Crystallogr (2010) 0.76
Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution. Comput Struct Biotechnol J (2015) 0.76
Rapid chain tracing of polypeptide backbones in electron-density maps. Acta Crystallogr D Biol Crystallogr (2010) 0.75
De Novo modeling in cryo-EM density maps with Pathwalking. J Struct Biol (2016) 0.75
Heterodimers as the Structural Unit of the T=1 Capsid of the Fungal Double-Stranded RNA Rosellinia necatrix Quadrivirus 1. J Virol (2016) 0.75
Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps. Methods Enzymol (2016) 0.75
Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps. Biomed Res Int (2017) 0.75
Three dimensional electron microscopy and in silico tools for macromolecular structure determination. EXCLI J (2013) 0.75
Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities. J Chem Theory Comput (2017) 0.75
UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem (2004) 112.47
The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science (2000) 28.25
EMAN: semiautomated software for high-resolution single-particle reconstructions. J Struct Biol (1999) 27.52
Structure of bacteriorhodopsin at 1.55 A resolution. J Mol Biol (1999) 8.17
The crystal structure of the bacterial chaperonin GroEL at 2.8 A. Nature (1994) 6.72
Crystal structure of the tyrosine kinase domain of the human insulin receptor. Nature (1995) 6.16
Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. J Struct Biol (1999) 5.71
The atomic structure of the bluetongue virus core. Nature (1998) 4.27
Conformational variability in the refined structure of the chaperonin GroEL at 2.8 A resolution. Nat Struct Biol (1995) 3.36
Seeing the herpesvirus capsid at 8.5 A. Science (2000) 3.35
Bridging the information gap: computational tools for intermediate resolution structure interpretation. J Mol Biol (2001) 3.29
100,000 protein structures for the biologist. Nat Struct Biol (1998) 3.19
Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions. Nat Struct Biol (2003) 2.76
Detecting folding motifs and similarities in protein structures. Methods Enzymol (1997) 2.63
Common ancestry of herpesviruses and tailed DNA bacteriophages. J Virol (2005) 2.60
The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins. Structure (2003) 2.53
Seeing GroEL at 6 A resolution by single particle electron cryomicroscopy. Structure (2004) 2.50
Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion. EMBO J (2001) 2.43
The pore structure of the closed RyR1 channel. Structure (2005) 2.42
Electron cryomicroscopy of biological machines at subnanometer resolution. Structure (2005) 2.15
The refined structure of a protein catenane: the HK97 bacteriophage capsid at 3.44 A resolution. J Mol Biol (2003) 2.11
A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure. J Mol Biol (1997) 2.10
Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus. Nat Struct Biol (2001) 1.99
A 9 angstroms single particle reconstruction from CCD captured images on a 200 kV electron cryomicroscope. J Struct Biol (2004) 1.70
Atomic coordinates for triose phosphate isomerase from chicken muscle. Biochem Biophys Res Commun (1976) 1.38
A Structural-informatics approach for tracing beta-sheets: building pseudo-C(alpha) traces for beta-strands in intermediate-resolution density maps. J Mol Biol (2004) 1.34
Structure of the herpesvirus major capsid protein. EMBO J (2003) 1.33
Structural biology of cellular machines. Trends Cell Biol (2006) 1.19
A structural-informatics approach for mining beta-sheets: locating sheets in intermediate-resolution density maps. J Mol Biol (2003) 1.13
Architecture of the herpes simplex virus major capsid protein derived from structural bioinformatics. J Mol Biol (2003) 1.05
Computing a family of skeletons of volumetric models for shape description. Comput Aided Des (2007) 1.03
NIH workshop on structural proteomics of biological complexes. Structure (2003) 0.87
Outcome of the first electron microscopy validation task force meeting. Structure (2012) 4.35
Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus. Nature (2006) 3.73
Paraneoplastic thrombocytosis in ovarian cancer. N Engl J Med (2012) 3.54
Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy. Nature (2008) 3.54
De novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure (2008) 3.41
EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res (2010) 3.32
Close membrane-membrane proximity induced by Ca(2+)-dependent multivalent binding of synaptotagmin-1 to phospholipids. Nat Struct Mol Biol (2006) 3.14
Protein structure fitting and refinement guided by cryo-EM density. Structure (2008) 3.12
Refinement of protein structures into low-resolution density maps using rosetta. J Mol Biol (2009) 2.94
The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state. Cell (2003) 2.89
Mechanism of folding chamber closure in a group II chaperonin. Nature (2010) 2.85
Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions. Nat Struct Biol (2003) 2.76
Interbilayer-crosslinked multilamellar vesicles as synthetic vaccines for potent humoral and cellular immune responses. Nat Mater (2011) 2.71
Common ancestry of herpesviruses and tailed DNA bacteriophages. J Virol (2005) 2.60
Remotely triggered liposome release by near-infrared light absorption via hollow gold nanoshells. J Am Chem Soc (2008) 2.56
Seeing GroEL at 6 A resolution by single particle electron cryomicroscopy. Structure (2004) 2.50
Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. J Struct Biol (2010) 2.48
The pore structure of the closed RyR1 channel. Structure (2005) 2.42
Outcome of a workshop on archiving structural models of biological macromolecules. Structure (2006) 2.32
Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis. Structure (2004) 2.30
Cryo-EM asymmetric reconstruction of bacteriophage P22 reveals organization of its DNA packaging and infecting machinery. Structure (2006) 2.26
4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement. Proc Natl Acad Sci U S A (2010) 2.17
Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. Nat Struct Mol Biol (2010) 2.12
Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. J Mol Biol (2006) 2.06
An expanded conformation of single-ring GroEL-GroES complex encapsulates an 86 kDa substrate. Structure (2006) 2.04
Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Proc Natl Acad Sci U S A (2011) 2.03
Direct electron detection yields cryo-EM reconstructions at resolutions beyond 3/4 Nyquist frequency. J Struct Biol (2012) 1.94
Structure of Halothiobacillus neapolitanus carboxysomes by cryo-electron tomography. J Mol Biol (2006) 1.90
Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm. J Struct Biol (2007) 1.90
The molecular architecture of the eukaryotic chaperonin TRiC/CCT. Structure (2012) 1.80
DNA packaging and delivery machines in tailed bacteriophages. Curr Opin Struct Biol (2007) 1.79
A digital atlas to characterize the mouse brain transcriptome. PLoS Comput Biol (2005) 1.78
4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus. EMBO J (2011) 1.77
Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure. Structure (2011) 1.71
Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography. J Mol Biol (2010) 1.71
A 9 angstroms single particle reconstruction from CCD captured images on a 200 kV electron cryomicroscope. J Struct Biol (2004) 1.70
Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel. Proc Natl Acad Sci U S A (2008) 1.68
Essential function of the built-in lid in the allosteric regulation of eukaryotic and archaeal chaperonins. Nat Struct Mol Biol (2007) 1.67
Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. J Struct Biol (2005) 1.67
Structural analysis of the anaphase-promoting complex reveals multiple active sites and insights into polyubiquitylation. Mol Cell (2005) 1.65
JADAS: a customizable automated data acquisition system and its application to ice-embedded single particles. J Struct Biol (2008) 1.62
Assessing the capabilities of a 4kx4k CCD camera for electron cryo-microscopy at 300kV. J Struct Biol (2006) 1.61
Zernike phase contrast cryo-electron microscopy and tomography for structure determination at nanometer and subnanometer resolutions. Structure (2010) 1.60
Structure of the acrosomal bundle. Nature (2004) 1.59
Cryo-EM of macromolecular assemblies at near-atomic resolution. Nat Protoc (2010) 1.58
3D volume reconstruction of a mouse brain from histological sections using warp filtering. J Neurosci Methods (2006) 1.51
Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT. Nat Struct Mol Biol (2008) 1.51
Applications of a bilateral denoising filter in biological electron microscopy. J Struct Biol (2003) 1.50
Mitochondrial ATP synthasome: three-dimensional structure by electron microscopy of the ATP synthase in complex formation with carriers for Pi and ADP/ATP. J Biol Chem (2004) 1.47
Interprotofilament interactions between Alzheimer's Abeta1-42 peptides in amyloid fibrils revealed by cryoEM. Proc Natl Acad Sci U S A (2009) 1.45
Electron cryotomography reveals the portal in the herpesvirus capsid. J Virol (2006) 1.40
Three-dimensional architecture of the rod sensory cilium and its disruption in retinal neurodegeneration. Cell (2012) 1.40
Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: a "horned" bacteriophage of marine synechococcus. J Mol Biol (2007) 1.37
Mitochondrial ATP synthasome. Cristae-enriched membranes and a multiwell detergent screening assay yield dispersed single complexes containing the ATP synthase and carriers for Pi and ADP/ATP. J Biol Chem (2003) 1.35
Automated segmentation of molecular subunits in electron cryomicroscopy density maps. J Struct Biol (2006) 1.34
Structure of the herpesvirus major capsid protein. EMBO J (2003) 1.33
Modeling protein structure at near atomic resolutions with Gorgon. J Struct Biol (2011) 1.29
Structure of Ca2+ release channel at 14 A resolution. J Mol Biol (2005) 1.27
Model of human low-density lipoprotein and bound receptor based on cryoEM. Proc Natl Acad Sci U S A (2009) 1.27
Structure of the type 1 inositol 1,4,5-trisphosphate receptor revealed by electron cryomicroscopy. J Biol Chem (2003) 1.26
Dual action of ATP hydrolysis couples lid closure to substrate release into the group II chaperonin chamber. Cell (2011) 1.25
Interactive separation of segmented bones in CT volumes using graph cut. Med Image Comput Comput Assist Interv (2008) 1.24
Flexible architecture of IP3R1 by Cryo-EM. Structure (2011) 1.24
Visualizing virus assembly intermediates inside marine cyanobacteria. Nature (2013) 1.20
Learning-based segmentation framework for tissue images containing gene expression data. IEEE Trans Med Imaging (2007) 1.17
Visualizing GroEL/ES in the act of encapsulating a folding protein. Cell (2013) 1.16
Determination of icosahedral virus structures by electron cryomicroscopy at subnanometer resolution. Adv Protein Chem (2003) 1.16
A geometric database for gene expression data. Symp Geom Process (2003) 1.15
Validation of cryo-EM structure of IP₃R1 channel. Structure (2013) 1.15
Visualizing the structural changes of bacteriophage Epsilon15 and its Salmonella host during infection. J Mol Biol (2010) 1.15
Tarsal and metatarsal bone mineral density measurement using volumetric quantitative computed tomography. J Digit Imaging (2008) 1.14
Cryo-EM model validation using independent map reconstructions. Protein Sci (2013) 1.13
Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle. EMBO J (2011) 1.12
Radiation damage effects at four specimen temperatures from 4 to 100 K. J Struct Biol (2009) 1.12
Structural mechanism of SDS-induced enzyme activity of scorpion hemocyanin revealed by electron cryomicroscopy. Structure (2009) 1.10
Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling. Proc Natl Acad Sci U S A (2013) 1.10
Object oriented database and electronic notebook for transmission electron microscopy. Microsc Microanal (2003) 1.10
Cryoelectron microscopy of protein IX-modified adenoviruses suggests a new position for the C terminus of protein IX. J Virol (2006) 1.09
Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density. PLoS Comput Biol (2006) 1.08
Volumetric quantitative computed tomography measurement precision for volumes and densities of tarsal and metatarsal bones. J Clin Densitom (2011) 1.07
Quaternary structure of human fatty acid synthase by electron cryomicroscopy. Proc Natl Acad Sci U S A (2001) 1.06
Architecture of the herpes simplex virus major capsid protein derived from structural bioinformatics. J Mol Biol (2003) 1.05
The skeletal muscle Ca2+ release channel has an oxidoreductase-like domain. Proc Natl Acad Sci U S A (2002) 1.04
An examination of the electrostatic interactions between the N-terminal tail of the Brome Mosaic Virus coat protein and encapsidated RNAs. J Mol Biol (2012) 1.04
Computing a family of skeletons of volumetric models for shape description. Comput Aided Des (2007) 1.03
Multifunctional RNA nanoparticles. Nano Lett (2014) 1.03
The 2010 cryo-EM modeling challenge. Biopolymers (2012) 1.02
TRiC's tricks inhibit huntingtin aggregation. Elife (2013) 1.02
Automated pipeline for atlas-based annotation of gene expression patterns: application to postnatal day 7 mouse brain. Methods (2009) 1.01
Reprogramming an ATP-driven protein machine into a light-gated nanocage. Nat Nanotechnol (2013) 1.00
Probing 3'-ssDNA loop formation in E. coli RecBCD/RecBC-DNA complexes using non-natural DNA: a model for "Chi" recognition complexes. J Mol Biol (2006) 0.99
Structure of triglyceride-rich human low-density lipoproteins according to cryoelectron microscopy. Biochemistry (2003) 0.98
Achievable resolution from images of biological specimens acquired from a 4k x 4k CCD camera in a 300-kV electron cryomicroscope. J Struct Biol (2008) 0.98
Manifold dual contouring. IEEE Trans Vis Comput Graph (2007) 0.98