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

CC BY-SA 4.0
2020-05-22T06:23:14.683Z
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?
djordje
CC BY-SA 4.0
2020-05-22T08:24:14.757Z
I am not sure what are the threshold or if there is a threshold or you look at literature
BND
CC BY-SA 4.0
2020-05-21T17:37:15.730Z
2020-05-21T17:37:15.730Z
BND
<p>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.</p>

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

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

<p>Best</p>

<database>
Calculating polarity and hydrophobicity of a ligand/small molecule
# Calculating polarity and hydrophobicity of a ligand/small molecule

(Asked by: username_0 on 2020-05-20)

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?

Best

**Tags:** database

---

## 1 answers

### Answer by username_1 on 2020-05-21. Score: 1 | Accepted answer

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

> **Comments:**
> **username_0**: 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?  
> **username_1**: I am not sure what are the threshold or if there is a threshold or you look at literature  

---

