PDB to FASTA: Extract a Sequence from Any Structure (Free)

By BioDockify Computational Research Team · September 3, 2026 · Tutorials

Extract a protein sequence from any PDB file as FASTA: RCSB, Open Babel and Biopython routes, SEQRES versus ATOM records, modified residues and gaps.

Read the complete article with tables, code and references on BioDockify.

Key References

• Berman HM et al. The Protein Data Bank. Nucleic Acids Res. 2000;28:235-242. doi:10.1093/nar/28.1.235
• Open Babel format conversion documentation, open-babel.readthedocs.io.
• Cock PJA et al. Biopython: freely available Python tools for computational molecular biology. Bioinformatics. 2009;25:1422-1423.

Scope & Limitations

Extracted sequences reflect the deposited construct, not necessarily the wild-type protein