EMDataResource
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EMDataResource
metasource: Fairsharing.org
version: None
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
formerly: EMDataBank
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
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EMDataResource
metasource: Fairsharing.orgversion: None
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
formerly: EMDataBank
metasource: re3data.orgversion: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
Other names: formerly: EMDataBank
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EMDataResource
metasource: Fairsharing.orgversion: None
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
formerly: EMDataBank
metasource: re3data.orgversion: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
Three-dimensional Electron Microscopy (3DEM) has become a key experimental method in structural biology for a broad spectrum of biological specimens from molecules to cells. The EMDataResource project provides a unified portal for deposition, retrieval and analysis of 3DEM density maps, atomic models and associated metadata.
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Three-dimensional Electron Microscopy (3DEM) has become a key experimental method in structural biology for a broad spectrum of biological specimens from molecules to cells. The EMDataResource project provides a unified portal for deposition, retrieval and analysis of 3DEM density maps, atomic models and associated metadata.
metasource: Fairsharing.orgversion: None
Cryo electron microscopy enables the determination of 3D structures of macromolecular complexes and cells from 2 to 100 Å resolution. EMDataResource is the unified global portal for one-stop deposition and retrieval of 3DEM density maps, atomic models and associated metadata, and is a joint effort among investigators of the Stanford/SLAC CryoEM Facility and the Research Collaboratory for Structural Bioinformatics (RCSB) at Rutgers, in collaboration with the EMDB team at the European Bioinformatics Institute. EMDataResource also serves as a resource for news, events, software tools, data standards, and validation methods for the 3DEM community. The major goal of the EMDataResource project in the current funding period is to work with the 3DEM community to (1) establish data-validation methods that can be used in the process of structure determination, (2) define the key indicators of a well-determined structure that should accompany every deposition, and (3) implement appropriate validation procedures for maps and map-derived models into a 3DEM validation pipeline.
metasource: re3data.orgversion: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
Webpage:
http://www.emdataresource.org/Webpage
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http://www.emdataresource.org/
metasource: Fairsharing.orgversion: None
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
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Public Domain
metasource: re3data.orgversion: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
Licence URL
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http://www.emdataresource.org/faq.html#c5
metasource: re3data.orgversion: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
Publications:
Publications
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Publications
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EMDataBank unified data resource for 3DEM
PubMed citations: 73.
73 articles citing: EMDataBank unified data resource for 3DEM
Protein Structural Modeling for Electron Microscopy Maps Using VESPER and MAINMAST. PMID:35849043
Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly. PMID:35831370
Validation analysis of EMDB entries. PMID:35503203
Search and sequence analysis tools services from EMBL-EBI in 2022. PMID:35412617
The intrinsically disordered TSSC4 protein acts as a helicase inhibitor, placeholder and multi-interaction coordinator during snRNP assembly and recycling. PMID:35188580
CR-I-TASSER: assemble protein structures from cryo-EM density maps using deep convolutional neural networks. PMID:35132244
Multiscale modelling of the extracellular matrix. PMID:35072037
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
New system for archiving integrative structures. PMID:34866606
Submission of structural biology data for review purposes. PMID:34866604
Submission of structural biology data for review purposes. PMID:34866597
The European Bioinformatics Institute (EMBL-EBI) in 2021. PMID:34850134
PDB-101: Educational resources supporting molecular explorations through biology and medicine. PMID:34601771
IsoExplorer: an isosurface-driven framework for 3D shape analysis of biomedical volume data. PMID:34429686
DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. PMID:34267316
EvoSeg: Automated Electron Microscopy Segmentation through Random Forests and Evolutionary Optimization. PMID:34206006
REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. PMID:34021280
From integrative structural biology to cell biology. PMID:33957123
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. PMID:33956157
Peroxiredoxins wear many hats: Factors that fashion their peroxide sensing personalities. PMID:33895094
VESPER: global and local cryo-EM map alignment using local density vectors. PMID:33828103
Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality. PMID:33823127
ProDy 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python. PMID:33822884
The actomyosin interface contains an evolutionary conserved core and an ancillary interface involved in specificity. PMID:33767187
Hybrid methods for combined experimental and computational determination of protein structure. PMID:33380110
Local and global analysis of macromolecular atomic displacement parameters. PMID:33021494
UCSF ChimeraX: Structure visualization for researchers, educators, and developers. PMID:32881101
State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps. PMID:32866476
The data universe of structural biology. PMID:32695409
Cryo-EM structure of arabinosyltransferase EmbB from Mycobacterium smegmatis. PMID:32636380
Shape-preserving elastic solid models of macromolecules. PMID:32407309
Evolving data standards for cryo-EM structures. PMID:32002441
Nano-encapsulated Escherichia coli Divisome Anchor ZipA, and in Complex with FtsZ. PMID:31822696
The structure and oxidation of the eye lens chaperone αA-crystallin. PMID:31792453
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. PMID:31780431
Structural Organization and Dynamics of Homodimeric Cytohesin Family Arf GTPase Exchange Factors in Solution and on Membranes. PMID:31601460
Cryo-EM map interpretation and protein model-building using iterative map segmentation. PMID:31599033
In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila. PMID:31498321
Cryo_fit: Democratization of flexible fitting for cryo-EM. PMID:31279069
Archiving and disseminating integrative structure models. PMID:31278630
High-resolution cryo-EM structures of outbreak strain human norovirus shells reveal size variations. PMID:31182604
Anticipating innovations in structural biology. PMID:30912485
Integration of macromolecular complex data into the Saccharomyces Genome Database. PMID:30715277
PIXER: an automated particle-selection method based on segmentation using a deep neural network. PMID:30658571
A call for public archives for biological image data. PMID:30377375
A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps. PMID:30377346
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. PMID:30357405
Comparing cryo-EM structures. PMID:30321594
Searching for 3D structural models from a library of biological shapes using a few 2D experimental images. PMID:30208849
Assessment of detailed conformations suggests strategies for improving cryoEM models: Helix at lower resolution, ensembles, pre-refinement fixups, and validation at multi-residue length scale. PMID:30107233
Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge. PMID:30063987
Updates to the RNA mapping database (RMDB), version 2. PMID:30053264
Computational Modeling of Hepatitis C Virus Envelope Glycoprotein Structure and Recognition. PMID:29892287
Automated map sharpening by maximization of detail and connectivity. PMID:29872005
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. PMID:29688351
Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules. PMID:29657133
Revising the Structural Diversity of Ribosomal Proteins Across the Three Domains of Life. PMID:29529322
Cryo-electron microscopy structure of a human PRMT5:MEP50 complex. PMID:29518110
Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors. PMID:29276036
Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER. PMID:29220075
Validation of Structures in the Protein Data Bank. PMID:29174494
CryoEM-based hybrid modeling approaches for structure determination. PMID:29107896
Steerable Principal Components for Space-Frequency Localized Images. PMID:29081879
Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model. PMID:28963369
Trends in the Electron Microscopy Data Bank (EMDB). PMID:28580912
Recent developments in the CCP-EM software suite. PMID:28580908
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. PMID:28573592
EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps. PMID:28572576
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. PMID:28190782
Databases and Archiving for CryoEM. PMID:27572735
Single-Particle Refinement and Variability Analysis in EMAN2.1. PMID:27572727
The archiving and dissemination of biological structure data. PMID:27450113
EMPIAR: a public archive for raw electron microscopy image data. PMID:27067018
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cell
metasource: Fairsharing.org
version: None
data model
metasource: Fairsharing.org
version: None
electron microscopy
metasource: Fairsharing.org
version: None
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
nucleic acid
metasource: Fairsharing.org
version: None
tissue
metasource: Fairsharing.org
version: None
validation
metasource: Fairsharing.org
version: None
viral sequence
metasource: Fairsharing.org
version: None
bioinformatics
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
biology
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
crystal growth
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
crystallography
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
crystals
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
electron distribution
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
electrons
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
microscopy
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
molecular biology
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
molecular microbiology
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
nuclear magnetic resonance
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
tomography
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
Tags
More detailed information about this field from each metasource.
cell
metasource: Fairsharing.orgversion: None
data model
metasource: Fairsharing.orgversion: None
electron microscopy
metasource: Fairsharing.orgversion: None
metasource: re3data.org
version: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
nucleic acid
metasource: Fairsharing.orgversion: None
tissue
metasource: Fairsharing.orgversion: None
validation
metasource: Fairsharing.orgversion: None
viral sequence
metasource: Fairsharing.orgversion: None
bioinformatics
metasource: re3data.orgversion: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
biology
metasource: re3data.orgversion: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
crystal growth
metasource: re3data.orgversion: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
crystallography
metasource: re3data.orgversion: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
crystals
metasource: re3data.orgversion: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
electron distribution
metasource: re3data.orgversion: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
electrons
metasource: re3data.orgversion: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
microscopy
metasource: re3data.orgversion: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
molecular biology
metasource: re3data.orgversion: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
molecular microbiology
metasource: re3data.orgversion: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
nuclear magnetic resonance
metasource: re3data.orgversion: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
tomography
metasource: re3data.orgversion: re3data.org: EMDataResource; editing status 2021-11-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3431F last accessed: 2022-11-04
cell data model electron microscopy nucleic acid tissue validation viral sequence bioinformatics crystal growth crystallography crystals electron distribution electrons microscopy molecular biology molecular microbiology nuclear magnetic resonance tomography
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