Protein-Ligand Interaction Fingerprints
ProLIF is a tool designed to generate Interaction FingerPrints (IFP) and compute similarity scores for protein-ligand interactions, given a reference ligand.
ProLIF is written in Python 3, and uses the following non-standard libraries:
- numpy
- rdkit
Make sure RDKit is installed before proceeding to the next step:
conda install -c rdkit rdkit
Once this is done, you can download and install the package with Pip:
pip install prolif
ProLIF is a command-line tool, so open a terminal and use the prolif command with the following arguments:
INPUT arguments:
-r fileName, --reference fileName
Path to your reference ligand.
-l fileName [fileName ...], --ligand fileName [fileName ...]
Path to your ligand(s).
-p fileName, --protein fileName
Path to your protein.
--residues RESIDUES [RESIDUES ...]
Residues chosen for the interactions. Default: automatically detect residues within --cutoff of the reference ligand
--cutoff float Cutoff distance for automatic detection of binding site residues. Default: 5.0 Å
--json fileName Path to a custom parameters file.
OUTPUT arguments:
-o filename, --output filename
Path to the output CSV file
--log level Set the level of the logger. Default: ERROR
-v, --version Show version and exit
Other arguments:
--interactions bit [bit ...]
List of interactions used to build the fingerprint.
│ Class Ligand Residue
│―――――――――――――――――――――――――――――――――――――――――――――
HBdonor │ Hydrogen bond donor acceptor
HBacceptor │ Hydrogen bond acceptor donor
XBdonor │ Halogen bond donor acceptor
XBacceptor │ Halogen bond acceptor donor
cation │ Ionic cation anion
anion │ Ionic anion cation
hydrophobic │ Hydrophobic hydrophobic hydrophobic
FaceToFace │ Pi-stacking aromatic aromatic
FaceToEdge │ Pi-stacking aromatic aromatic
pi-cation │ Pi-cation aromatic cation
cation-pi │ Pi-cation cation aromatic
MBdonor │ Metal metal ligand
MBacceptor │ Metal ligand metal
Default: HBdonor HBacceptor cation anion FaceToFace FaceToEdge hydrophobic
--score {tanimoto,dice,tversky}
Similarity score between molecule A and B :
Let 'a' and 'b' be the number of bits activated in molecules A and B, and 'c' the number of activated bits in common.
-) tanimoto : c/(a+b-c). Used by default
-) dice : 2c/(a+b)
-) tversky : c/(alpha*(a-c)+beta*(b-c)+c)
--alpha int Alpha parameter for Tversky. Default: 0.7
--beta int Beta parameter for Tversky. Default: 0.3
Mandatory arguments: --reference --ligand --protein
MOL2 files only.
Unless otherwise noted, all files in this directory and all subdirectories are distributed under the Apache License, Version 2.0:
Copyright 2017-2018 Cédric BOUYSSET
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
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