3DBionotes Cross-app

External Annotations

External annotations - Display custom annotations for a PDB, EMDB or UniProt entry
https://3dbionotes.cnb.csic.es?queryId=:id&annotations_url=:url

:id > PDB / EMDB / UniProt (e.g. 1acb, emd-2924, P01112)
:url > URL annotations request (e.g. "https://[your_server_here].cnb.csic.es/pdb/external_annotations.json")

External Structure

External protein struture - Display external structure and optional annotations
https://3dbionotes.cnb.csic.es/programmatic/autofetch?url=:structure_url&annotations_url=:annotations_url&title=:name

:structure_url > URL structure request (e.g. http://[your_server_here].cnb.csic.es/pdb/1ACB.pdb )
:annotations_url > URL annotations request (optional, e.g. http://[your_server_here].cnb.csic.es/pdb/external_annotations.json )
:name > STRING title of the submission (e.g. "my title")

3DBionotes API

EMDB info

Source -  PDBe REST API

available - Check if a particular EMDB entry is available
https://3dbionotes.cnb.csic.es/api/info/EMDB/available/:emdb_id

size - Get the voxels size of a EMDB entry
https://3dbionotes.cnb.csic.es/api/info/EMDB/size/:emdb_id

data - Get map threshold and grid limits
https://3dbionotes.cnb.csic.es/api/info/EMDB/data/:emdb_id

title - Get EMDB entry title
https://3dbionotes.cnb.csic.es/api/info/EMDB/title/:emdb_id

UniProt info

Source -  UniProt API

sequence - Get UniProt accession sequence
https://3dbionotes.cnb.csic.es/api/info/Uniprot/:uniprot_acc

title - Get UniProt accession title
https://3dbionotes.cnb.csic.es/api/info/UniprotTitle/:uniprot_acc

PDB info

Source -  PDBe REST API

available - Check if a particular PDB entry is available
https://3dbionotes.cnb.csic.es/api/info/PDB/available/:pdb_id

title - Get PDB entry title
https://3dbionotes.cnb.csic.es/api/info/PDB/title/:pdb_id

EMDB mappings

Source -  PDBe REST API

fitted PDB - Get fitted PDB IDs for a particular EMDB entry
https://3dbionotes.cnb.csic.es/api/mappings/EMDB/PDB/:emdb_id

UniProt mappings

Source -  PDBe REST API

UniProt to PDB structures - Get all the PDB structures associated to a UniProt accession
https://3dbionotes.cnb.csic.es/api/mappings/Uniprot/PDB/:uniprot_acc

UniProt to ENSEMBL transcripts - Get all the ENSEMBL transcripts associated to a UniProt accession
https://3dbionotes.cnb.csic.es/api/mappings/Uniprot/ENSEMBL/transcript/:uniprot_acc