AlphaFold Database Structure Extractor: A web server and API to download AlphaFold structures using common protein accessions

The AlphaFoldDB Structure Extractor is an open-access web server and API toolkit designed to facilitate the bulk download of predicted protein structures from the AlphaFold Database using well-known accession numbers. Addressing the current limitations in extracting structures beyond a restricted list of model organisms and a threshold number, this tool accepts diverse input identifiers, such as NCBI Taxonomy ID, RefSeq accessions, locus tags, and UniProt or AlphaFold accessions, and maps them to UniProt and AlphaFold IDs for structure retrieval. Users can download structure files in PDB, mmCIF, bCIF, or PAE JSON formats. The tool also generates an accompanying ID mapping file to trace input identifiers back to standard accession numbers and reports unmapped IDs separately. An API methodology is also provided for programmatic access, enabling integration into bioinformatics pipelines. AlphaFoldDB Structure Extractor streamlines the structure procurement process from AlphaFold database, empowering researchers in structural and functional genomics with minimal computational expertise. Availability and implementation: AlphaFoldDB Structure Extractor is freely available as a webserver at https://project.iith.ac.in/sharmaglab/alphafoldextractor/ for downloading structure coordinate files based on the user-provided input of protein accessions. The tool can be accessed programmatically using the API service we have provided.