EMDataBank.org
EMDataBank.org is a resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes.
Description
More detailed information about this field from each metasource.
EMDataBank.org is a resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:17.585340
Webpage:
http://EMDataBank.orgWebpage
More detailed information about this field from each metasource.
Publications:
Publications
More detailed information about this field from each metasource.
EMDataBank.org: unified data resource for CryoEM
PMID: 20935055
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:17.585340
Publications
More detailed information about this field from each metasource.
EMDataBank.org: unified data resource for CryoEM
PMID: 20935055
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:17.585340
-
EMDataBank.org: unified data resource for CryoEM
PubMed citations: 128.
128 articles citing: EMDataBank.org: unified data resource for CryoEM
Progressive assembly of multi-domain protein structures from cryo-EM density maps. PMID:35844960
Analysis of β-strand Twist from the 3-dimensional Image of a Protein. PMID:35838360
How advances in cryo-electron tomography have contributed to our current view of bacterial cell biology. PMID:35252838
Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology. PMID:35063097
High-resolution structures of the actomyosin-V complex in three nucleotide states provide insights into the force generation mechanism. PMID:34812732
Spatial arrangement of proteins in planar and curved membranes by PPM 3.0. PMID:34716622
Validation, analysis and annotation of cryo-EM structures. PMID:34473085
The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing. PMID:34048576
Making the invisible enemy visible. PMID:33972785
Detecting Protein Communities in Native Cell Extracts by Machine Learning: A Structural Biologist's Perspective. PMID:33937337
Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching. PMID:33825706
Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB. PMID:33744287
Local computational methods to improve the interpretability and analysis of cryo-EM maps. PMID:33623015
Data-driven challenges and opportunities in crystallography. PMID:33523208
Modeling the Influenza A NP-vRNA-Polymerase Complex in Atomic Detail. PMID:33477938
Improving SARS-CoV-2 structures: Peer review by early coordinate release. PMID:33460600
CERES: a cryo-EM re-refinement system for continuous improvement of deposited models. PMID:33404525
Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding. PMID:33402206
Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution. PMID:33277481
Progressive and accurate assembly of multi-domain protein structures from cryo-EM density maps. PMID:33083802
Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures. PMID:33063791
Density modification of cryo-EM maps. PMID:33021493
Improvement of cryo-EM maps by density modification. PMID:32807957
Validation tests for cryo-EM maps using an independent particle set. PMID:32743544
The data universe of structural biology. PMID:32695409
Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures. PMID:32676604
Current approaches for automated model building into cryo-EM maps using Buccaneer with CCP-EM. PMID:32496215
Cylindrical Similarity Measurement for Helices in Medium-Resolution Cryo-Electron Microscopy Density Maps. PMID:32216344
Wild-Type IDH1 and Mutant IDH1 Opposingly Regulate Podoplanin Expression in Glioma. PMID:32208352
Evolving data standards for cryo-EM structures. PMID:32002441
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. PMID:31780431
Aldehyde-alcohol dehydrogenase forms a high-order spirosome architecture critical for its activity. PMID:31586059
Conserved Central Intraviral Protein Interactome of the Herpesviridae Family. PMID:31575665
Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. PMID:31199794
ETDB-Caltech: A blockchain-based distributed public database for electron tomography. PMID:30986271
Deep Learning for Validating and Estimating Resolution of Cryo-Electron Microscopy Density Maps †. PMID:30917528
Anticipating innovations in structural biology. PMID:30912485
MBIR: A cryo-ET 3D reconstruction method that effectively minimizes missing wedge artifacts and restores missing information. PMID:30872095
Challenges and opportunities in cryo-EM single-particle analysis. PMID:30804214
New tools for the analysis and validation of cryo-EM maps and atomic models. PMID:30198894
Machine Learning Methods for X-Ray Scattering Data Analysis from Biomacromolecular Solutions. PMID:29874600
FragFit: a web-application for interactive modeling of protein segments into cryo-EM density maps. PMID:29788317
CHALLENGES IN MATCHING SECONDARY STRUCTURES IN CRYO-EM: AN EXPLORATION. PMID:29770261
Worldwide Protein Data Bank validation information: usage and trends. PMID:29533231
A fragment based method for modeling of protein segments into cryo-EM density maps. PMID:29132296
Integrative structure modeling with the Integrative Modeling Platform. PMID:28960548
Combinatorial peptide-based epitope mapping from Ebola virus DNA vaccines and infections reveals residue-level determinants of antibody binding. PMID:28922082
New tools and functions in data-out activities at Protein Data Bank Japan (PDBj). PMID:28815765
Reconstituted IMPDH polymers accommodate both catalytically active and inactive conformations. PMID:28794265
The Image Data Resource: A Bioimage Data Integration and Publication Platform. PMID:28775673
Bayesian Modeling of Biomolecular Assemblies with Cryo-EM Maps. PMID:28382301
The NIH 3D Print Exchange: A Public Resource for Bioscientific and Biomedical 3D Prints. PMID:28367477
Variability of Protein Structure Models from Electron Microscopy. PMID:28262392
Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix. PMID:27936925
Empowering pharmacoinformatics by linked life science data. PMID:27830428
PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. PMID:27710935
Databases and Archiving for CryoEM. PMID:27572735
Condor: a simulation tool for flash X-ray imaging. PMID:27504081
HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1. PMID:27384951
Comparison of an Atomic Model and Its Cryo-EM Image at the Central Axis of a Helix. PMID:27280059
An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images. PMID:27008671
Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment. PMID:26988127
Web-based volume slicer for 3D electron-microscopy data from EMDB. PMID:26876163
Conserved Intramolecular Interactions Maintain Myosin Interacting-Heads Motifs Explaining Tarantula Muscle Super-Relaxed State Structural Basis. PMID:26851071
Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling. PMID:26846888
MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature. PMID:26753741
γ-TEMPy: Simultaneous Fitting of Components in 3D-EM Maps of Their Assembly Using a Genetic Algorithm. PMID:26655474
EMDataBank unified data resource for 3DEM. PMID:26578576
Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution. PMID:26557958
Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB. PMID:26508754
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. PMID:26476444
Validation methods for low-resolution fitting of atomic structures to electron microscopy data. PMID:26116787
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. PMID:26095030
Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research. PMID:26087941
The Caltech Tomography Database and Automatic Processing Pipeline. PMID:26087141
Sequential myosin phosphorylation activates tarantula thick filament via a disorder-order transition. PMID:26038232
Navigating 3D electron microscopy maps with EM-SURFER. PMID:26025554
Localize.pytom: a modern webserver for cryo-electron tomography. PMID:25934806
Improved cryoEM-Guided Iterative Molecular Dynamics--Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction. PMID:25883538
MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography. PMID:25882513
Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions. PMID:25615868
Collaborative computational project for electron cryo-microscopy. PMID:25615866
Protein structure annotation resources. PMID:25502191
The complex portal--an encyclopaedia of macromolecular complexes. PMID:25313161
A 3D cellular context for the macromolecular world. PMID:25289590
The Protein Data Bank archive as an open data resource. PMID:25062767
LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry. PMID:25032790
High-resolution views of TRPV1 and their implications for the TRP channel superfamily. PMID:24961977
Enhancing UCSF Chimera through web services. PMID:24861624
Towards an integrative structural biology approach: combining Cryo-TEM, X-ray crystallography, and NMR. PMID:24748171
Elastic properties and heterogeneous stiffness of the phi29 motor connector channel. PMID:24655509
Estimating loop length from CryoEM images at medium resolutions. PMID:24565041
High-affinity gold nanoparticle pin to label and localize histidine-tagged protein in macromolecular assemblies. PMID:24560806
Modeling protein assemblies in the proteome. PMID:24445405
Intensity-based skeletonization of CryoEM gray-scale images using a true segmentation-free algorithm. PMID:24384713
Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change. PMID:24333899
PDBe: Protein Data Bank in Europe. PMID:24288376
Mass spectrometry coupled experiments and protein structure modeling methods. PMID:24132151
Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB. PMID:24113529
Targeted conformational search with map-restrained self-guided Langevin dynamics: application to flexible fitting into electron microscopic density maps. PMID:23876978
Likelihood-based classification of cryo-EM images using FREALIGN. PMID:23872434
Computational methods for constructing protein structure models from 3D electron microscopy maps. PMID:23796504
SFG analysis of surface bound proteins: a route towards structure determination. PMID:23727992
Hsc70-induced changes in clathrin-auxilin cage structure suggest a role for clathrin light chains in cage disassembly. PMID:23710728
The role of structural bioinformatics resources in the era of integrative structural biology. PMID:23633580
Enterotoxigenic Escherichia coli CS1 pilus: not one structure but several. PMID:23354749
Trendspotting in the Protein Data Bank. PMID:23337870
Data management challenges in three-dimensional EM. PMID:23211764
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. PMID:23203869
The RCSB Protein Data Bank: new resources for research and education. PMID:23193259
Creating a community resource for protein science. PMID:22969036
The Coherent X-ray Imaging Data Bank. PMID:22936162
Implementing an X-ray validation pipeline for the Protein Data Bank. PMID:22505268
OMERO: flexible, model-driven data management for experimental biology. PMID:22373911
Outcome of the first electron microscopy validation task force meeting. PMID:22325770
Direct electron detection yields cryo-EM reconstructions at resolutions beyond 3/4 Nyquist frequency. PMID:22285189
Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PMID:22272186
Towards an atlas of mammalian cell ultrastructure by cryo soft X-ray tomography. PMID:22155291
PDBe: Protein Data Bank in Europe. PMID:22110033
Consensus among flexible fitting approaches improves the interpretation of cryo-EM data. PMID:22019767
Stepwise expansion of the bacteriophage ϕ6 procapsid: possible packaging intermediates. PMID:22019738
The DARC site: a database of aligned ribosomal complexes. PMID:22009674
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. PMID:21976737
A unified convention for biological assemblies with helical symmetry. PMID:21795813
MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map. PMID:21715383
BCL::EM-Fit: rigid body fitting of atomic structures into density maps using geometric hashing and real space refinement. PMID:21565271
The Protein Data Bank in Europe (PDBe): bringing structure to biology. PMID:21460450
The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:21177655
Tags:
Tags
More detailed information about this field from each metasource.
imaging
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:17.585340
structure analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:17.585340
proteins
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:17.585340
mapping
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:17.585340
molecular modelling
metasource: bio.tools
version: extracted_at: 2022-11-04T11:34:17.585340
Tags
More detailed information about this field from each metasource.
imaging
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:17.585340
structure analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:17.585340
proteins
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:17.585340
mapping
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:17.585340
molecular modelling
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:34:17.585340
imaging structure analysis proteins mapping molecular modelling
Need help integrating and/or managing biomedical data?