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.
Installation
pip install psearch
Dependency
pmapper >= 0.2
Example
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.
- 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 prepare_datatset.py -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 prepare_datatset.py -h
- Model building.
python3 psearch.py -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
TODO
Documentation
All scripts have `-h' argument to retrieve descriptions of all available options and arguments.
Authors
Alina Kutlushina, Pavel Polishchuk
Citation
Ligand-Based Pharmacophore Modeling Using Novel 3D Pharmacophore Signatures
Alina Kutlushina, Aigul Khakimova, Timur Madzhidov, Pavel Polishchuk
Molecules 2018, 23(12), 3094
https://doi.org/10.3390/molecules23123094
License
BSD-3 clause
Project details
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