I have lot of SMILES IDs of the ligands. What I am interested in is the polarity and hydrophobicity score of each of the ligands.

In other words, does ligand have more polar groups and can it make more polar interactions or is it more hydrophobic?

Does anybody know the way/software to look at it?



1 Answer 1


You can calculate their polar surface area or logo using rdkit or openbabel. Other molecular properties may be available as well.

  • $\begingroup$ I see, you mean like TPSA of the molecule? Also, is there some cutoff that can be used there, in a way like TPSA of 100-150+ is considered that molecule is polar, while TPSA<100 is considered as hydrophobic molecule? $\endgroup$
    – djordje
    May 22, 2020 at 6:23
  • $\begingroup$ I am not sure what are the threshold or if there is a threshold or you look at literature $\endgroup$
    – BND
    May 22, 2020 at 8:24

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