AlphaFold Database Structure Extractor: a web server and API to download AlphaFold structures using common protein accessions
Open accessPublished version of a preprint
Abstract
BACKGROUND: The AlphaFoldDB Structure Extractor ( https://project.iith.ac.in/sharmaglab/alphafoldextractor/ ) 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 formats. Addressing the current limitations in extracting structures beyond a restricted list of model organisms and a threshold number, this tool accepts diverse sequence and structure input identifiers, such as NCBI Taxonomy ID, RefSeq accessions, locus tags (old and new), and UniProt or AlphaFold accessions for structure retrieval. RESULTS: Users can download structure files in PDB, mmCIF, bCIF, or/and PAE JSON formats using any of the above-mentioned input accessions as input. The tool also generates an accompanying ID mapping file to trace input identifiers back to standard accession numbers and reports unmapped IDs separately. Users can also perform just the ID mapping in case they do not require the structure coordinate files. An API methodology is also provided for programmatic access, enabling integration into bioinformatics pipelines. We have tested the tool using several randomly selected accessions (individual inputs and up to 5000 input accessions) of each type from NCBI RefSeq and Taxonomy Databases, UniProt Database and AlphaFold Database. CONCLUSIONS: Overall, AlphaFoldDB Structure Extractor streamlines the structure procurement process from AlphaFold database, empowering researchers in structural and functional genomics with minimal computational expertise.
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Cites
Highly accurate protein structure prediction with AlphaFold
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Rawool, S. R., & Sharma, G. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.11.724241
“CheA structures download, prediction, alignment and comparison: 25 out of 154 CheA structures, available on AlphaFold database, were downloaded using AlphFoldStructureExtractor tool (Saraf et al., 2025).”
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“The predicted three‑dimensional structure of EmTPx (AlphaFold Server) [22] was visualized using PyMOL [23], and the positions of the core epitopes were located and highlighted within the structural model.”
- Authors
- Saraf, N., Karthik, V., & Sharma, G.
- Affiliations
- Indian Institute of Technology Hyderabad (IN)
- Corresponding author
- Sharma, Gaurav
- Venue
- BMC Bioinformatics
- Published
- 2025-11-25
- Volume
- 26
- Issue
- 1
- Pages
- 305-305
- ISSN
- 1471-2105 (ISSN-L)
- PMC
- PMC12751494
- OpenAlex
- W4416675739
- Semantic Scholar
- 1b788a668b3cdc01809d52f697ca19321c21f3ac
- Cited by
- 4
- References
- 9
- Citations by year
- 2026: 4
- FWCI
- 1.20
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Bioinformatics (publishedVersion, cc-by-nc-nd)
- Research Square (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Science and Engineering Research Board (Start-up Research Grant (SRG))
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- AlphaFold, protein structure prediction, web server, API, reference sequences, UniProt, locus tags, ID mapping, Protein Data Bank, mmCIF, structural genomics
- MeSH terms
- Protein Conformation, Proteins, Software, User-Computer Interface, Protein Folding, Computational Biology, Internet, Databases, Protein
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