Preparation of the protein input files for PLANTS

The program PLANTS needs a .mol2 protein file format thus our procedure protonates the uploaded .pdb structure file by using the program PDBPQR (version 1.6; ref1) with AMBER forcefield option. Then, the pdb file is converted into a .mol2 file format.


 Protonate the protein and convert it into .mol2 file
  • Protein structure file in pdb format:  
    •  
  • (option) Create a binding site input file around a residue or a ligand in the pdb structure:

    RESIDUE name (case sensitive)   RESIDUE number   CHAIN (or leave empty)

    or set coordinates of the center of the binding site: x ,   y ,   z

    Binding site radius


    •  or simply convert a protein .pdb file into .mol2 file
  • Protein structure file in pdb format  

    The residue naming scheme must be of AMBER type; the protonation step is skipped

    •  

    References

    (1) Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research 32 W665-W667 2004. doi: 10.1093/nar/gkh381