Open Access
Bioinformatics, volume 35, issue 8, pages 1334-1341
Development of a protein–ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions
1
Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, Warsaw, Poland
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2
Publication type: Journal Article
Publication date: 2018-09-08
Journal:
Bioinformatics
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 5.8
ISSN: 13674803, 13674811, 14602059
Biochemistry
Computer Science Applications
Molecular Biology
Statistics and Probability
Computational Mathematics
Computational Theory and Mathematics
Abstract
Fingerprints (FPs) are the most common small molecule representation in cheminformatics. There are a wide variety of FPs, and the Extended Connectivity Fingerprint (ECFP) is one of the best-suited for general applications. Despite the overall FP abundance, only a few FPs represent the 3D structure of the molecule, and hardly any encode protein-ligand interactions.Here, we present a Protein-Ligand Extended Connectivity (PLEC) FP that implicitly encodes protein-ligand interactions by pairing the ECFP environments from the ligand and the protein. PLEC FPs were used to construct different machine learning models tailored for predicting protein-ligand affinities (pKi∕d). Even the simplest linear model built on the PLEC FP achieved Rp = 0.817 on the Protein Databank (PDB) bind v2016 'core set', demonstrating its descriptive power.The PLEC FP has been implemented in the Open Drug Discovery Toolkit (https://github.com/oddt/oddt).Supplementary data are available at Bioinformatics online.
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Wójcikowski M. et al. Development of a protein–ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions // Bioinformatics. 2018. Vol. 35. No. 8. pp. 1334-1341.
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Wójcikowski M., Kukiełka M., Stepniewska Dziubinska M., Siedlecki P. Development of a protein–ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions // Bioinformatics. 2018. Vol. 35. No. 8. pp. 1334-1341.
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TY - JOUR
DO - 10.1093/bioinformatics/bty757
UR - https://doi.org/10.1093/bioinformatics/bty757
TI - Development of a protein–ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions
T2 - Bioinformatics
AU - Wójcikowski, Maciej
AU - Kukiełka, Michał
AU - Stepniewska Dziubinska, Marta
AU - Siedlecki, Pawel
PY - 2018
DA - 2018/09/08
PB - Oxford University Press
SP - 1334-1341
IS - 8
VL - 35
SN - 1367-4803
SN - 1367-4811
SN - 1460-2059
ER -
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@article{2018_Wójcikowski,
author = {Maciej Wójcikowski and Michał Kukiełka and Marta Stepniewska Dziubinska and Pawel Siedlecki},
title = {Development of a protein–ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions},
journal = {Bioinformatics},
year = {2018},
volume = {35},
publisher = {Oxford University Press},
month = {sep},
url = {https://doi.org/10.1093/bioinformatics/bty757},
number = {8},
pages = {1334--1341},
doi = {10.1093/bioinformatics/bty757}
}
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Wójcikowski, Maciej, et al. “Development of a protein–ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions.” Bioinformatics, vol. 35, no. 8, Sep. 2018, pp. 1334-1341. https://doi.org/10.1093/bioinformatics/bty757.