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3DBIONOTES CROSS-APP

EXTERNAL ANNOTATIONS

External annotations - Display custom annotations for a PDB, EMDB or UniProt entry
http://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. http://cantor.cnb.csic.es/pdb/external_annotations.json )

EXTERNAL STRUCTURE

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

:structure_url > URL structure request (e.g. http://cantor.cnb.csic.es/pdb/1ACB.pdb )
:annotations_url > URL annotations request (optional, e.g. http://cantor.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
http://3dbionotes.cnb.csic.es/api/info/EMDB/available/:emdb_id

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

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

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

UniProt info

Source - UniProt API

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

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

PDB info

Source - PDBe REST API

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

title - Get PDB entry title
http://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
http://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
http://3dbionotes.cnb.csic.es/api/mappings/Uniprot/PDB/:uniprot_acc

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

PDB mappings

Source - PDBe REST API

PDB to UniProt - Get the UniProt accessions related to the chains of a particular PDB entry
http://3dbionotes.cnb.csic.es/api/mappings/PDB/Uniprot/:pdb_id

PDB alignments

Source - PDBe REST API

PDB to UniProt sequence alignment - Sequence alignment between a PDB entry and the related UniProt accessions
http://3dbionotes.cnb.csic.es/api/alignments/PDB/:pdb_id

ENSEMBL alignments

Source - ENSEMBL REST API

ENSEMBL to UniProt sequence alignment - Protein sequence alignment between a ENSEMBL transcript and a related UniProt accession
http://3dbionotes.cnb.csic.es/api/alignments/ENSEMBL/:ensembl_gene_id/:ensembl_transcript_id/:uniprot_acc

Annotations

UniProt annotations - Get UniProt annotations for a particular UniProt accession
Source - UniProt API
http://3dbionotes.cnb.csic.es/api/annotations/EBI/features/:uniprot_acc

IEDB annotations - Get IEDB annotations for a particular UniProt accession
Source - Immune Epitope DB
http://3dbionotes.cnb.csic.es/api/annotations/IEDB/Uniprot/:uniprot_acc

PhosphoSitePlus annotations - Get PhosphoSitePlus annotations for a particular UniProt accession
Source - PhosphoSitePlus
http://3dbionotes.cnb.csic.es/api/annotations/Phosphosite/Uniprot/:uniprot_acc

BioMuta annotations - Get BioMuta annotations for a particular UniProt accession
Source - BioMuta
http://3dbionotes.cnb.csic.es/api/annotations/Phosphosite/Uniprot/:uniprot_acc

dSysMap annotations - Get dSysMap annotations for a particular UniProt accession
Source - dSysMap
http://3dbionotes.cnb.csic.es/api/annotations/dsysmap/Uniprot/:uniprot_acc