Structure based pharmacophore and protein-ligand interactions

[Daniel-Ibarrola]

Currently structure based pharmacophores are extracted by using protein-ligand interactions using the library plip, however plip was not conceived for pharmacophore extraction and it seems to have issues with hydrophobic features in the context of pharmacophores. Moreover, plip needs a pdb file to obtain the protein-ligand interactions which is impractical and slow when extracting pharmacophores from a molecular dynamics trajectory.

To solve this we need to search if there are any alternatives to plip. If not, we'll probably have to implement the pharmacophore extraction from the protein-ligand complex.

[dprada]

I agree. Implementing the pharmacophore extraction here would entail some benefits in the future.

[orgw]

ACP4 (https://github.com/tsudalab/ACP4) provides code for extracting pharmacophores.