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Method for creating POPS, PROFILE and POCKETS for Graphsite

  • Cavity center with their respective PDB IDs are given in cavity_centers.csv
  • All the data were created using python3.8

Prerequisites

Steps

1. Download PDBs

  • Using RSCB PDB batch download services download files. (https://www.rcsb.org/downloads)
    • Files will be downloaded as *.ent.gz
    unzip *.ent.gz -d path_to_extract_directory
mv file.ent pathto_files/file.pdb

2. Separate PDB chains into different PDBs and renumber residues

  • separate_pdb_chains.py will separate PDB chains into different PDB files
  • renumber.py will renumber residues in PDB files. Note that renumber.py will delete files that could not be renumbered. 
    mkdir PDB_CHAINS
python separate_pdb_chains.py
python renumber.py
  • Note: Please ensure installation of pdbtools in the system before the use of separate_pdb_chains.py

3. Run POPScomp

  • Use chain PDB files to run POPScomp 
    cd PDB_CHAINS
for file in *.pdb; do pops --pdb $file --atomOut --popsOut $file.pops; done
  • Note: Please ensure installation of POPScomp in the system before the use of pops

4. Convert PDB to FASTA

  • This script converts PDB to FASTA 
    python pdb2seq.py

5. Run PROFILpro 1.2

  • This program uses the FASTA sequences as input and generates protein PROFILES
  • SCRATCH-1D_1.3 can be downloaded from https://download.igb.uci.edu
    • num_rounds are limited to either 2, 3 or 4
    • num_threads: default 4
    for file in *.fa; do sh SCRATCH-1D_1.3/pkg/PROFILpro_1.2/bin/generate_profiles.sh $file $file.profile num_rounds num_threads; done

6. Calculate POCKETS

  • FPOCKET 4.0 uses PDB files to find all pockets in a protein
  • FPOCKET generates file_out folder for each of the PDBs
  • POCKET PDBs generated by FPOCKET can be found in file_out/pockets 
    for file in *.pdb; do fpocket -f $file; done

7. Transform the POCKETS

  • Create POCKETS_UNTRANSFORMED
  • Move all the POCKET PDBs generated by FPOCKET into POCKETS_UNTRANSFORMED
  • This script aligns POCKET center to origin (0, 0, 0) and aligns principal axes with eigen vectors 
    mkdir POCKETS_TRANSFORMED
python rotate_translate.py

8. Convert POCKET PDBs to MOL2

  • Convert POCKET PDBs to MOL2 using obabel 3.1.1 
    cd POCKETS_TRANSFORMED
for v in *_rot.pdb; do obabel -ipdb $v -omol2 -gen3d -O$v.mol2; done
mkdir POCKETS_TRANSFORMED_MOL2
mv *.mol2 POCKETS_TRANSFORMED_MOL2