The 3D-Beacons resource has undergone some major improvements, including updates to the API and a new sequence search feature.

The 3D-Beacons Network, originally announced in September 2021, brings together experimentally determined and predicted protein structure models, alongside relevant quality metrics, from several providers and makes them freely available in one place. The data are provided by a number of services, including the Protein Data Bank in Europe (PDBe), AlphaFold DB, SWISS-MODEL, Protein Ensemble Database (PED), Small Angle Scattering Biological Data Bank (SASBDB), Genome3D, and PDBe Knowledge Base (PDBe-KB). 3D-Beacons allows users to search using UniProt accession and access protein structure models from all these different providers in a standardised format.

This new update to the 3D-Beacons resource includes some major improvements to the infrastructure and the public website (3d-beacons.org). The API that serves the underlying data has been updated to version 2.4.2. This is a non-breaking change and now supports POST queries to the summary endpoint, up to a maximum of 10 accessions. You can find more information about the available calls in the API documentation at https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/. 

Another big update is the addition of a brand new sequence search feature, allowing users to easily find relevant structures based on an input protein sequence. The sequence search process uses the NCBI blastp tool, hosted by EBI, to query the sequence against the UniProtKB database and find all the similar proteins and obtain the available structures containing those proteins. Once the job is submitted, a job ID is returned to the users which can be used in the results endpoint to access the models. The annotations endpoint now supports the retrieval of 14 different types of annotations for a UniProt accession.

Visit the 3D-Beacons website to explore the data and learn more about the resource at 3d-beacons.org.