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Amino acids inventory

This program generates an inventory of amino acids present on the surface of peripheral proteins of a same family.
(See report.pdf and presentation.pdf for more details)

Prerequisites

UNIX/shell environment
Python3, R, PyMOL

Running the program with the current cases

$./launch.sh

Then choose a CATH superfamily (3.20.20.190 or 2.29.30.29)

Menu items

  1. Display the structural alignment colored by secondary structure
  2. Display the structural alignment in PyMOL
  3. Study of a fold/loop (gives out a csv file of all amino acids)
  4. Add sequences to the structural alignment
  5. Generate a plot (amino acid inventory)
  6. Delete unused files and Quit

Add a new case

  1. Choose a CATH superfamily (http://www.cathdb.info/) and create a directory /superfamilies/NEW-FAMILY
  2. Provide a structural alignment file (FASTA format) /NEW-FAMILY/fasta/cath/alignment.fasta
  3. Provide the pdb files corresponding /NEW-FAMILY/pdb
  4. Provide a file containing sequences to add (FASTA format) : /NEW-FAMILY/fasta/new/seq_to_align.fasta
  5. In the header of the python script (/scripts/script.py) indicate the superfamily studied, the model chosen and the different secondary structures to analyse (name, type and number in the sequence)

Authors

  • Hélène Kabbech - Bioinformatics Master student (University of Paris Diderot)
  • Internship supervised by Prof. Nathalie Reuter (CBU Bergen)