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

2. 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

2. Download a list of PDBs

python3 ../download_pdbs.py

3. 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

2. Download a list of PDBs

python3 ../download_pdbs.py

3. Identify disulfide bonds

python3 ../calculate_disulfides.py

Map PDB residues to UniProt protein sequences

1. Move into the mapping directory

cd pdb_protein_mapping

2. 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.