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CSD-peptide

This repository contains several utilities for finding and processing peptide structures deposited in the CDC small molecule database. Two main scripts are included:

  • fetch_ccdc.py : A script for finding all possible peptide-containing structures in the CSD. Requires CSD and the python bindings to be installed.
  • convert.py : A script that a) identifies all CSD structures that contain peptides, and b) writes them as "PDB-style"

Notes on convert.py

  • Usage: convert.py [--minlen MINLEN] pdbs
  • the "MINLEN" argument only generates peptides of at least the given length
  • the folder refpep/canonic contains all the AAs of which the script is aware. The folder refpep/peptoid contains all the peptoids of which the script is aware.
  • "automatic" assignment of other AAs/peptoids will be made with peptoids assigned the tag N## and AAs the tag A##
  • outputs are found in converted
  • currently only alpha AAs, N-methylated alpha AAs, and peptoids are understood. Additional variants may be added in the future.