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Protein Structure Annotations

About

PDB structures for proteins with PDB annotations can be downloaded and parsed for amino acid numbering and residue names. SIFTS files, providing residue level mapping between PDB sequences and protein sequences, were downloaded for each PDB. Cysteines resolved in each PDB were mapped to their appropriate UniProt protein sequence and identifiers for PDB to UniProt pairs were created: PDB_C#_UniProtKBID_C#.

Set Up

  1. Import modules
pip3 install biopython xmlschema freesasa
  1. Prepare a text file with PDB identifiers <pdbs_to_download.txt>

Usage

Calculate the solvent accessibility of each residue in a list of PDBs according to the FreeSASA package

  1. Move into the solvent accessibility directory
cd solvent_accessibility_calculations
  1. Download a list of PDBs
python3 ../download_pdbs.py
  1. Calculate the solvent accessibilities
python3 ../calculate_sasa.py

Identify if each residue in a list of PDBs is involved in a disulfide bond

  1. Move into the disulfide directory
cd disulfide_bonds
  1. Download a list of PDBs
python3 ../download_pdbs.py
  1. Identify disulfide bonds
python3 ../calculate_disulfides.py

Map PDB residues to UniProt protein sequences

  1. Move into the mapping directory
cd pdb_protein_mapping
  1. Download and map SIFTS
python3 ../parse_sifts.py

Citation

  1. Boatner LM, Palafox MF, Schweppe DK, Backus KM. CysDB: a human cysteine database based on experimental quantitative chemoproteomics. Cell Chem Biol. 2023 Jun 15;30(6):683-698.e3. doi: 10.1016/j.chembiol.2023.04.004. Epub 2023 Apr 28. PMID: 37119813; PMCID: PMC10510411.