EMDB Search Engine documentation
Text Search
You can use the search bar near the top of all EMDB pages to search across any data deposited at EMDB and EMPIAR.
The EMDB search engine was built using the Apache Solr server, therefore you can check the Solr query parser tutorial to find further information about how to use this engine. You can also check the full list of EMDB query fields.
Query Syntax
Free text terms
Most of the text fields are broken up into single words before indexing. This procedure allows you to perform searches based on single terms or phrases (using double quotes).
The search below returns all the entries that contain the word "zika" anywhere:
The search below returns all the entries that contain the phrase "monoclonal antibody" anywhere:
Boolean operators
More complex queries can be created by combining multiple terms and boolean operators.
Boolean operator | Description | Example |
---|---|---|
AND | Both terms are required. | spliceosome AND human |
OR | One of the terms is required. | spliceosome OR ribonucleoprotein |
NOT | The following term must not be present. | NOT Relion |
The search terms can be grouped to form sub-queries and parentheses are used to define the order of the sub-queries. The query below returns all entries that contain the words spliceosome or ribonucleoprotein, but do not contain the word human.
"(spliceosome OR ribonucleoprotein) AND NOT human"
Search by specific fields
Searching by specific fields allows the user to obtain more confident results. All you need to do is specify the field followed by a colon (":") and the term that you are searching for within the field. All the query syntax previously described is also available for specific-field searches. The full list of fields and their description can be found here.
An example to find all the human spliceosomes or ribonucleoproteins, using the sample name and the human taxonomy ID: 9606:
(sample_name:ribonucleoprotein OR sample_name:spliceosome) AND natural_source_ncbi_code:9606
Range Search
The search egnine allows the user to find entries that fall within a given range. The upper and lower bounds must be provided in the following format: "[X TO Y]". The example below finds all entries with a resolution value between 1Å and 3Å.
You can also use curly brackets to set exclusive range intervals. In the example below we are retrieving all entries with resolution value between 1Å and 3Å, but excluding entries with exactly 3Å resolution.
Range queries are not restricted to numeric fields, it is possible to search over date and text ranges. You can find the Solr documentation about date formats here. The example below returns all entries that contain samples starting with the letter "X", "Y" or "Z".
An asterisk ("*") can be used as to match any values. It can be included in a range query to define an infinite interval. The example below finds all entries with resolution value greater than or equal to 20Å.
Another use of the asterisk is to match every entry that has a value for that field. The example below list all entries that contain half-maps:
Fuzzy Search
The EMDB search engine allows the user to search by similar terms using the Damerau-Levenshtein Distance (basically, the number of edit operations necessary to transform one string in another). To perform a fuzzy search, you need to add the tilde symbol ("~") after the query term followed by the maximum distance. The example below will match any sample term that is at most one text edit from the word DNA. In other words, it will return all entries containing samples of DNA or RNA.
Quick links
Recent Entries
(Show all)Cryo-EM structure of an E. coli rotated ribosome bound with RF3-GDPCP and p/E-tRNAPhe (State II-C)
Cryo-EM structure of an E. coli rotated ribosome bound with RF3-GDPCP and p/E-tRNAPhe (Composite state II-B)
Complex of NPR1 ectodomain and REGN5381 Fab in an active-like state with no ANP bound
Cryo-EM structure of an E. coli rotated ribosome bound with RF3-GDPCP and p/E-tRNAPhe (State II-B)
Phosphorylated, ATP-bound, inhibitor 172-bound E1371Q human cystic fibrosis transmembrane conductance regulator
RF3-GDPCP bound to an E. coli non-rotated ribosome termination complex, from focused classification and refinement (State II-A)
Complex of NPR1 ectodomain with ANP plus an allosteric activating antibody, REGN5381
Structure of HCoV-HKU1C spike in the functionally anchored-1up conformation with 1TMPRSS2
Cryo-EM structure of human ABCC4 in complex with ANP-bound in NBD1 and METHOTREXATE
Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 3TMPRSS2
Structure of HCoV-HKU1C spike in the functionally anchored-2up conformation with 2TMPRSS2
Structure of HCoV-HKU1A spike in the functionally anchored-3up conformation with 3TMPRSS2
Local structure of HCoV-HKU1C spike in complex with TMPRSS2 and glycan
Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 2TMPRSS2
Local structure of HCoV-HKU1A spike in complex with TMPRSS2 and glycan
Structure of HCoV-HKU1C spike in the glycan-activated-closed conformation
Structure of HCoV-HKU1C spike in the glycan-activated-2up conformation
Structure of HCoV-HKU1C spike in the glycan-activated-1up conformation
Structure of HCoV-HKU1C spike in the glycan-activated-3up conformation
ICP1 Csy-dsDNA-Cas1-Cas2/3 complex (fully assembled form), C2 symmetry
CryoEM structure of the transketolase ANIP from Streptomyces hygrospinosus
ICP1 Csy-dsDNA-Cas1-Cas2/3 complex (fully assembled form) composited structure with C1 symmetry
Trimeric prM/E spike of Tick-borne encephalitis virus immature particle
Cryo-electron tomogram of small unilamellar vesicles decorated with poliovirus protein 2C
Archaellum filament from the Halobacterium salinarum deltaAgl27 strain
Cryo EM map of the type 2A polymorph of alpha-synuclein at pH 7.0.
Tick-borne encephalitis virus (strain Neudoerfl) immature particle
Archaellum filament from the Halobacterium salinarum deltaAgl26 strain
Structure of human terminal uridylyltransferase 4 (TUT4, ZCCHC11) in complex with pre-let7g miRNA and Lin28A
Subtomogram average of 80S ribosomes in S. cerevisiae under acute glucose starvation
Cryo EM structure of the type 3B polymorph of alpha-synuclein at low pH.
DIV 1 hippocampal neuron (weighted back-projection and greyscale segmentation)
MicroED structure of SARS-CoV-2 main protease (MPro/3CLPro) with missing cone eliminated by suspended drop
ApoRF3 bound to an E. coli non-rotated ribosome termination complex, from focused classification and refinement (State I-B)
Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with RF1, P- and E-site tRNAPhe (State I-A)
RF3-GDPCP bound to an E. coli rotated ribosome, from focused classification and refinement (State II-C)
Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with RF1, P- and E-site tRNAPhe (State II-D)
Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with apoRF3, RF1, P- and E-site tRNAPhe (State I-B)
Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with RF3-GDPCP, RF1, P- and E-site tRNAPhe (Composite state II-A)
Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with RF3-GDPCP, RF1, P- and E-site tRNAPhe (State II-A)
Cryo-EM structure of an E. coli rotated ribosome bound with RF3-GDPCP and p/E-tRNAPhe (Composite state II-C)
Phosphorylated, ATP-bound, E1371Q human cystic fibrosis transmembrane conductance regulator (E1371Q-CFTR)
Cryo-EM structure of alpha5beta1 integrin in complex with NeoNectin
RF3-GDPCP bound to an E. coli rotated ribosome, from focused classification and refinement (State II-B)
Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with apoRF3, RF1, P- and E-site tRNAPhe (Composite state I-B)