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PSearch: ligand-based pharmacophore modeling and screening

Project description

PSearch - 3D ligand-based pharmacophore modeling

PSearch is a tool to automatically generate 3D ligand-based pharmacophore models.


pip install psearch


pmapper >= 0.3.1


Creation of ligand-based pharmacophore models

It is recommended to create an empty dir which would be your $PROJECT_DIR and copy an input file to that location.
There are two steps of pharmacophore model generation.

  1. Data set preparation. It takes as input a comma-separated SMILES file containing SMILES, compound id, activity value. It splits the input on active and inactive subsets, generates stereoisomers and conformers, creates databases of active and inactive compounds with labeled pharmacophore features.
python3 -i $PROJECT_DIR/input.smi -l 6 -u 8 -c 4

-i - path to the input file;
-u - threshold to define active compounds (compounds with activity value >= threshold are considered active);
-l - threshold to define inactive compounds (compounds with activity value <= threshold are considered inactive);
-c - number of CPUs to use.
There are other arguments available to tweak data set preparation. To get the full list of arguments run python3 -h

  1. Model building.
python3 -p $PROJECT_DIR -t 0.4 -c 4

-p - path to the project dir;
-t - threshold for compound clustering to create training sets;
-c- number of CPUs to use

Virtual screening with pharmacophore models



All scripts have `-h' argument to retrieve descriptions of all available options and arguments.


Alina Kutlushina, Pavel Polishchuk


Ligand-Based Pharmacophore Modeling Using Novel 3D Pharmacophore Signatures
Alina Kutlushina, Aigul Khakimova, Timur Madzhidov, Pavel Polishchuk
Molecules 2018, 23(12), 3094


BSD-3 clause

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