LigGen: A Tool for Predicting Water Positions in Proteins.

To create a drug-like chemical space for a specific binding pocket of protein,it is important to take into account not only the topology of the protein's amino acids, but also their local environment-at least water molecules. In this article, we have written a Python program that predicts the position of water molecules (oxygen atoms) in protein crystals. The algorithm also sorts the predicted oxygen atoms based on their polarity coefficients. The user can change: the length of the hydrogen bonds between the most electronegative atoms (N, O, S) of amino acids and water oxygen; the accuracy of prediction; number of processor cores as well as program parameters. LigGen is available at: https://github.com/e-shstkv/LigGen.