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Lennard Jones Potential of a Protein PDB in python
Proteins crystal structures in pdb format can be downloaded from the RCSB database. A docking function contains two components, an electrostatic component computed with poisson boltzman and a lennard jones component. We spoke about this in an earlier post called Protein Ligand Interaction Fingerprints. I was thinking about writing a function that used the protein ligand interaction fingerprint to calculate these potentials but you could probably just calculate it by parsing the PDB file. I would think the protein ligand interaction fingerprint would be better for screening a large number of docked compounds initially. In fact I found a code on github that did just that. It calculates the lennard jones potential of the entire protein for all its atoms, which is not what we want. However it gives you the basic idea of how you could do this for just the atoms in the protein that interact with the ligand. First I will give you the code and then I can give you the pseudocode for how we can expand on this.
- ReadProtein. Write a function whose input is the name of a file containing the positions of all atoms of a protein. A pdb file contains all the info you need so you must parse it in python.