Published in Nucleic Acids Res on October 08, 2010
The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res (2012) 5.73
Outcome of the first electron microscopy validation task force meeting. Structure (2012) 4.35
OMERO: flexible, model-driven data management for experimental biology. Nat Methods (2012) 3.72
PDBe: Protein Data Bank in Europe. Nucleic Acids Res (2011) 3.03
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure (2015) 2.93
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. Nucleic Acids Res (2012) 2.61
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. Nucleic Acids Res (2011) 2.57
Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol (2012) 2.37
PDBe: Protein Data Bank in Europe. Nucleic Acids Res (2013) 2.16
Direct electron detection yields cryo-EM reconstructions at resolutions beyond 3/4 Nyquist frequency. J Struct Biol (2012) 1.94
Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions. Acta Crystallogr D Biol Crystallogr (2015) 1.89
The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. Nucleic Acids Res (2011) 1.79
Implementing an X-ray validation pipeline for the Protein Data Bank. Acta Crystallogr D Biol Crystallogr (2012) 1.79
The Coherent X-ray Imaging Data Bank. Nat Methods (2012) 1.78
Likelihood-based classification of cryo-EM images using FREALIGN. J Struct Biol (2013) 1.72
The Protein Data Bank in Europe (PDBe): bringing structure to biology. Acta Crystallogr D Biol Crystallogr (2011) 1.21
The Protein Data Bank archive as an open data resource. J Comput Aided Mol Des (2014) 1.20
Data management challenges in three-dimensional EM. Nat Struct Mol Biol (2012) 1.19
Trendspotting in the Protein Data Bank. FEBS Lett (2013) 1.19
The role of structural bioinformatics resources in the era of integrative structural biology. Acta Crystallogr D Biol Crystallogr (2013) 1.15
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. Nucleic Acids Res (2015) 1.14
A 3D cellular context for the macromolecular world. Nat Struct Mol Biol (2014) 1.12
Enhancing UCSF Chimera through web services. Nucleic Acids Res (2014) 1.09
EMDataBank unified data resource for 3DEM. Nucleic Acids Res (2015) 0.98
Stepwise expansion of the bacteriophage ϕ6 procapsid: possible packaging intermediates. J Mol Biol (2011) 0.96
BCL::EM-Fit: rigid body fitting of atomic structures into density maps using geometric hashing and real space refinement. J Struct Biol (2011) 0.95
Towards an atlas of mammalian cell ultrastructure by cryo soft X-ray tomography. J Struct Biol (2011) 0.94
Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB. J Struct Biol (2013) 0.93
Elastic properties and heterogeneous stiffness of the phi29 motor connector channel. Biophys J (2014) 0.91
The complex portal--an encyclopaedia of macromolecular complexes. Nucleic Acids Res (2014) 0.91
Collaborative computational project for electron cryo-microscopy. Acta Crystallogr D Biol Crystallogr (2015) 0.88
Computational methods for constructing protein structure models from 3D electron microscopy maps. J Struct Biol (2013) 0.87
Modeling protein assemblies in the proteome. Mol Cell Proteomics (2014) 0.87
Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change. J Struct Biol (2013) 0.87
Navigating 3D electron microscopy maps with EM-SURFER. BMC Bioinformatics (2015) 0.86
MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map. Nucleic Acids Res (2011) 0.86
Consensus among flexible fitting approaches improves the interpretation of cryo-EM data. J Struct Biol (2011) 0.86
MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography. J Struct Biol (2015) 0.85
SFG analysis of surface bound proteins: a route towards structure determination. Phys Chem Chem Phys (2013) 0.83
Conserved Intramolecular Interactions Maintain Myosin Interacting-Heads Motifs Explaining Tarantula Muscle Super-Relaxed State Structural Basis. J Mol Biol (2016) 0.83
The NIH 3D Print Exchange: A Public Resource for Bioscientific and Biomedical 3D Prints. 3D Print Addit Manuf (2014) 0.82
Creating a community resource for protein science. Protein Sci (2012) 0.81
Improved cryoEM-Guided Iterative Molecular Dynamics--Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction. J Chem Theory Comput (2015) 0.81
The Caltech Tomography Database and Automatic Processing Pipeline. J Struct Biol (2015) 0.80
Targeted conformational search with map-restrained self-guided Langevin dynamics: application to flexible fitting into electron microscopic density maps. J Struct Biol (2013) 0.80
LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry. PLoS Comput Biol (2014) 0.80
Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research. Adv Mater (2015) 0.80
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
Sequential myosin phosphorylation activates tarantula thick filament via a disorder-order transition. Mol Biosyst (2015) 0.79
The DARC site: a database of aligned ribosomal complexes. Nucleic Acids Res (2011) 0.79
Towards an integrative structural biology approach: combining Cryo-TEM, X-ray crystallography, and NMR. J Struct Funct Genomics (2014) 0.79
Intensity-based skeletonization of CryoEM gray-scale images using a true segmentation-free algorithm. IEEE/ACM Trans Comput Biol Bioinform (2014) 0.79
Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment. Methods (2016) 0.79
Estimating loop length from CryoEM images at medium resolutions. BMC Struct Biol (2013) 0.78
Databases and Archiving for CryoEM. Methods Enzymol (2016) 0.78
High-resolution views of TRPV1 and their implications for the TRP channel superfamily. Handb Exp Pharmacol (2014) 0.78
Condor: a simulation tool for flash X-ray imaging. J Appl Crystallogr (2016) 0.77
Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB. Bioinformatics (2015) 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
Validation methods for low-resolution fitting of atomic structures to electron microscopy data. Arch Biochem Biophys (2015) 0.77
Hsc70-induced changes in clathrin-auxilin cage structure suggest a role for clathrin light chains in cage disassembly. Traffic (2013) 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
Mass spectrometry coupled experiments and protein structure modeling methods. Int J Mol Sci (2013) 0.76
Localize.pytom: a modern webserver for cryo-electron tomography. Nucleic Acids Res (2015) 0.76
HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1. Mol Cell Proteomics (2016) 0.76
γ-TEMPy: Simultaneous Fitting of Components in 3D-EM Maps of Their Assembly Using a Genetic Algorithm. Structure (2015) 0.76
Web-based volume slicer for 3D electron-microscopy data from EMDB. J Struct Biol (2016) 0.76
Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution. Comput Struct Biotechnol J (2015) 0.76
Retracted High-affinity gold nanoparticle pin to label and localize histidine-tagged protein in macromolecular assemblies. Structure (2014) 0.75
Enterotoxigenic Escherichia coli CS1 pilus: not one structure but several. J Bacteriol (2013) 0.75
A unified convention for biological assemblies with helical symmetry. Acta Crystallogr D Biol Crystallogr (2011) 0.75
MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature. BMC Bioinformatics (2016) 0.75
Bayesian Modeling of Biomolecular Assemblies with Cryo-EM Maps. Front Mol Biosci (2017) 0.75
PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. Acta Crystallogr D Struct Biol (2016) 0.75
Empowering pharmacoinformatics by linked life science data. J Comput Aided Mol Des (2016) 0.75
Variability of Protein Structure Models from Electron Microscopy. Structure (2017) 0.75
Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling. Biophys J (2016) 0.75
The Image Data Resource: A Bioimage Data Integration and Publication Platform. Nat Methods (2017) 0.75
Reconstituted IMPDH polymers accommodate both catalytically active and inactive conformations. Mol Biol Cell (2017) 0.75
Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr (2004) 227.01
UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem (2004) 112.47
The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol (1977) 90.57
Announcing the worldwide Protein Data Bank. Nat Struct Biol (2003) 17.06
Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J Mol Biol (1990) 13.72
Structure of dengue virus: implications for flavivirus organization, maturation, and fusion. Cell (2002) 9.13
Structure of the dengue virus envelope protein after membrane fusion. Nature (2004) 7.97
Visualizing density maps with UCSF Chimera. J Struct Biol (2006) 5.75
Variable surface epitopes in the crystal structure of dengue virus type 3 envelope glycoprotein. J Virol (2005) 3.58
Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome. Mol Cell (2008) 3.58
Structural basis of West Nile virus neutralization by a therapeutic antibody. Nature (2005) 3.51
Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases. Mol Cell (2008) 3.49
Structure of West Nile virus. Science (2003) 3.48
De novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure (2008) 3.41
AstexViewer: a visualisation aid for structure-based drug design. J Comput Aided Mol Des (2002) 3.29
Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. Structure (2007) 3.16
Protein structure fitting and refinement guided by cryo-EM density. Structure (2008) 3.12
Using Situs for the integration of multi-resolution structures. Biophys Rev (2010) 3.07
Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation. Cell (2005) 2.97
Refinement of protein structures into low-resolution density maps using rosetta. J Mol Biol (2009) 2.94
Mechanism of folding chamber closure in a group II chaperonin. Nature (2010) 2.85
ATP-bound states of GroEL captured by cryo-electron microscopy. Cell (2001) 2.84
Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J Struct Biol (2004) 2.78
Common ancestry of herpesviruses and tailed DNA bacteriophages. J Virol (2005) 2.60
Identification of secondary structure elements in intermediate-resolution density maps. Structure (2007) 2.60
Ab initio resolution measurement for single particle structures. J Struct Biol (2006) 2.53
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
Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography. Methods (2009) 2.39
Three-dimensional structure of the myosin V inhibited state by cryoelectron tomography. Nature (2006) 2.39
Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function. Cell (2009) 2.32
Data deposition and annotation at the worldwide protein data bank. Mol Biotechnol (2008) 2.30
The molecular architecture of cadherins in native epidermal desmosomes. Nature (2007) 2.29
Untangling desmosomal knots with electron tomography. Science (2003) 2.25
New electron microscopy database and deposition system. Trends Biochem Sci (2002) 2.17
Electron cryomicroscopy of biological machines at subnanometer resolution. Structure (2005) 2.15
Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. Nat Struct Mol Biol (2010) 2.12
N-linked glycosylation of west nile virus envelope proteins influences particle assembly and infectivity. J Virol (2005) 2.00
The beginning of kinesin's force-generating cycle visualized at 9-A resolution. J Cell Biol (2007) 1.97
Sharpening high resolution information in single particle electron cryomicroscopy. J Struct Biol (2008) 1.93
Combining X-ray crystallography and electron microscopy. Structure (2005) 1.88
Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology. J Struct Biol (2005) 1.56
Three-dimensional structure of the ion-coupled transport protein NhaA. Nature (2000) 1.53
Applications of a bilateral denoising filter in biological electron microscopy. J Struct Biol (2003) 1.50
The RecA hexamer is a structural homologue of ring helicases. Nat Struct Biol (1997) 1.47
Structure of an apoptosome-procaspase-9 CARD complex. Structure (2010) 1.42
Structure of hepatitis E virion-sized particle reveals an RNA-dependent viral assembly pathway. J Biol Chem (2010) 1.40
Automated segmentation of molecular subunits in electron cryomicroscopy density maps. J Struct Biol (2006) 1.34
Electron cryotomography of Tula hantavirus suggests a unique assembly paradigm for enveloped viruses. J Virol (2010) 1.33
A recombinant envelope protein vaccine against West Nile virus. Vaccine (2005) 1.31
A different conformation for EGC stator subcomplex in solution and in the assembled yeast V-ATPase: possible implications for regulatory disassembly. Structure (2008) 1.28
EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information. J Struct Biol (2003) 1.28
Biomolecular pleiomorphism probed by spatial interpolation of coarse models. Bioinformatics (2008) 1.24
Capturing a flavivirus pre-fusion intermediate. PLoS Pathog (2009) 1.24
Using VMD: an introductory tutorial. Curr Protoc Bioinformatics (2008) 1.19
Mechanism of replication machinery assembly as revealed by the DNA ligase-PCNA-DNA complex architecture. Proc Natl Acad Sci U S A (2009) 1.16
Representation of viruses in the remediated PDB archive. Acta Crystallogr D Biol Crystallogr (2008) 1.08
From electron microscopy to X-ray crystallography: molecular-replacement case studies. Acta Crystallogr D Biol Crystallogr (2007) 1.07
YUP.SCX: coaxing atomic models into medium resolution electron density maps. J Struct Biol (2008) 1.06
The structure of gene product 6 of bacteriophage T4, the hinge-pin of the baseplate. Structure (2009) 1.02
Distinct in situ structures of the Borrelia flagellar motor. J Struct Biol (2009) 1.02
4.6A Cryo-EM reconstruction of tobacco mosaic virus from images recorded at 300 keV on a 4k x 4k CCD camera. J Struct Biol (2010) 1.00
Analyses of subnanometer resolution cryo-EM density maps. Methods Enzymol (2010) 0.95
Cryo-electron microscopy reconstructions of two types of wild rabbit hemorrhagic disease viruses characterized the structural features of Lagovirus. Protein Cell (2010) 0.91
Global conformational changes of ribosome observed by normal mode fitting for 3D Cryo-EM structures. Structure (2009) 0.91
Rubisco in complex with Rubisco large subunit methyltransferase. Proc Natl Acad Sci U S A (2009) 0.90
Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions. Acta Crystallogr D Biol Crystallogr (2010) 0.90
Depositing electron microscopy maps. Structure (2003) 0.88
Backbone trace of partitivirus capsid protein from electron cryomicroscopy and homology modeling. Biophys J (2010) 0.87
Hybrid molecular structure of the giant protease tripeptidyl peptidase II. Nat Struct Mol Biol (2010) 0.84
A database for 'em. Nat Struct Biol (2003) 0.80
Inference of macromolecular assemblies from crystalline state. J Mol Biol (2007) 44.95
Announcing the worldwide Protein Data Bank. Nat Struct Biol (2003) 17.06
EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol (2006) 14.70
The Protein Data Bank. Acta Crystallogr D Biol Crystallogr (2002) 14.44
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res (2006) 13.44
The Protein Data Bank: unifying the archive. Nucleic Acids Res (2002) 12.37
The Protein Data Bank and structural genomics. Nucleic Acids Res (2003) 8.34
The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res (2005) 7.81
The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res (2010) 7.68
The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res (2004) 7.03
The RCSB PDB information portal for structural genomics. Nucleic Acids Res (2006) 6.36
CAPRI: a Critical Assessment of PRedicted Interactions. Proteins (2003) 6.36
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA (2008) 5.94
Towards complete validated models in the next generation of ARP/wARP. Acta Crystallogr D Biol Crystallogr (2004) 5.90
The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res (2012) 5.73
PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods (2011) 5.01
Remediation of the protein data bank archive. Nucleic Acids Res (2007) 4.89
SPARX, a new environment for Cryo-EM image processing. J Struct Biol (2006) 4.66
Outcome of the first electron microscopy validation task force meeting. Structure (2012) 4.35
TargetDB: a target registration database for structural genomics projects. Bioinformatics (2004) 4.17
Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus. Nature (2006) 3.73
OMERO: flexible, model-driven data management for experimental biology. Nat Methods (2012) 3.72
PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics (2004) 3.64
The RNA Ontology Consortium: an open invitation to the RNA community. RNA (2006) 3.60
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
A new generation of crystallographic validation tools for the protein data bank. Structure (2011) 3.41
De novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure (2008) 3.41
The European Bioinformatics Institute's data resources. Nucleic Acids Res (2003) 3.34
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
Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. Acta Crystallogr D Biol Crystallogr (2004) 3.11
Refinement of protein structures into low-resolution density maps using rosetta. J Mol Biol (2009) 2.94
Catabolite activator protein: DNA binding and transcription activation. Curr Opin Struct Biol (2004) 2.91
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
Structural basis of transcription activation: the CAP-alpha CTD-DNA complex. Science (2002) 2.67
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. Nucleic Acids Res (2012) 2.61
Common ancestry of herpesviruses and tailed DNA bacteriophages. J Virol (2005) 2.60
Identification of secondary structure elements in intermediate-resolution density maps. Structure (2007) 2.60
Evaluation of targeted next-generation sequencing-based preimplantation genetic diagnosis of monogenic disease. Fertil Steril (2013) 2.59
Remotely triggered liposome release by near-infrared light absorption via hollow gold nanoshells. J Am Chem Soc (2008) 2.56
BioJS: an open source JavaScript framework for biological data visualization. Bioinformatics (2013) 2.53
Seeing GroEL at 6 A resolution by single particle electron cryomicroscopy. Structure (2004) 2.50
MSDmotif: exploring protein sites and motifs. BMC Bioinformatics (2008) 2.48
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
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res (2003) 2.37
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
Data deposition and annotation at the worldwide protein data bank. Mol Biotechnol (2008) 2.30
Cryo-EM asymmetric reconstruction of bacteriophage P22 reveals organization of its DNA packaging and infecting machinery. Structure (2006) 2.26
UniChem: a unified chemical structure cross-referencing and identifier tracking system. J Cheminform (2013) 2.23
Ligand Depot: a data warehouse for ligands bound to macromolecules. Bioinformatics (2004) 2.21
New electron microscopy database and deposition system. Trends Biochem Sci (2002) 2.17
MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active sites. Proteins (2005) 2.17
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
PDBe: Protein Data Bank in Europe. Nucleic Acids Res (2013) 2.16
Electron cryomicroscopy of biological machines at subnanometer resolution. Structure (2005) 2.15
Pound-wise but penny-foolish: How well do micromolecules fare in macromolecular refinement? Structure (2003) 2.14
Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. Angew Chem Int Ed Engl (2003) 2.13