AlphaFoldDB Structure Extractor

AlphaFoldDB Structure Extractor downloads predicted protein structures from the AlphaFold Database using diverse protein accession formats to facilitate bulk structure retrieval for structural and functional genomics research.

Key Features:

• Multi-format accession input: Accepts NCBI Taxonomy ID, RefSeq accessions, locus tags (old and new), UniProt accessions, and AlphaFold accessions as input identifiers for structure retrieval.
• Multiple structure file formats: Downloads structure files in PDB, mmCIF, bCIF, and/or PAE JSON formats.
• ID mapping generation: Produces an accompanying ID mapping file to trace input identifiers back to standard accession numbers and reports unmapped IDs separately.
• Standalone ID mapping: Supports performing only ID mapping without downloading structure coordinate files.
• API access: Provides an API methodology for programmatic access and integration into bioinformatics pipelines.
• Bulk processing capability: Tested with individual inputs and up to 5000 input accessions of each type from NCBI RefSeq, NCBI Taxonomy, UniProt, and AlphaFold Databases.

Scientific Applications:

• Structural genomics: Enables bulk acquisition of predicted protein structures from the AlphaFold Database for large-scale structural analysis.
• Functional genomics: Supports retrieval of protein structures using common gene and protein accessions to facilitate functional annotation studies.
• Bioinformatics pipeline integration: Allows programmatic structure procurement through API for automated workflows.
• Cross-database identifier resolution: Maps diverse accession formats to standard identifiers for interoperability between NCBI RefSeq, NCBI Taxonomy, UniProt, and AlphaFold resources.

Methodology:

The tool accepts diverse sequence and structure input identifiers and retrieves corresponding predicted protein structures from the AlphaFold Database; an API methodology is provided for programmatic access.