Open Access
graphDelta: MPNN Scoring Function for the Affinity Prediction of Protein–Ligand Complexes
Dmitry S Karlov
1
,
Sergey Sosnin
1, 2
,
Vadim V. Fedorov
1, 2, 3
,
Maxim V Fedorov
1, 2, 3
,
Petr A. Popov
1, 4
,
Petr Popov
1, 4
2
Skolkovo Innovation Center,Syntelly LLC, 42 Bolshoy Boulevard, Moscow 143026, Russia
|
Publication type: Journal Article
Publication date: 2020-03-09
scimago Q1
wos Q2
SJR: 0.773
CiteScore: 7.1
Impact factor: 4.3
ISSN: 24701343
PubMed ID:
32201802
General Chemistry
General Chemical Engineering
Abstract
In this work, we present graph-convolutional neural networks for the prediction of binding constants of protein–ligand complexes. We derived the model using multi task learning, where the target variables are the dissociation constant (Kd), inhibition constant (Ki), and half maximal inhibitory concentration (IC50). Being rigorously trained on the PDBbind dataset, the model achieves the Pearson correlation coefficient of 0.87 and the RMSE value of 1.05 in pK units, outperforming recently developed 3D convolutional neural network model Kdeep.
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Metrics
85
Total citations:
85
Citations from 2024:
37
(43%)
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GOST
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Karlov D. S. et al. graphDelta: MPNN Scoring Function for the Affinity Prediction of Protein–Ligand Complexes // ACS Omega. 2020. Vol. 5. No. 10. pp. 5150-5159.
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Karlov D. S., Sosnin S., Fedorov V. V., Fedorov M. V., Popov P. A., Popov P. graphDelta: MPNN Scoring Function for the Affinity Prediction of Protein–Ligand Complexes // ACS Omega. 2020. Vol. 5. No. 10. pp. 5150-5159.
Cite this
RIS
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TY - JOUR
DO - 10.1021/acsomega.9b04162
UR - https://pubs.acs.org/doi/10.1021/acsomega.9b04162
TI - graphDelta: MPNN Scoring Function for the Affinity Prediction of Protein–Ligand Complexes
T2 - ACS Omega
AU - Karlov, Dmitry S
AU - Sosnin, Sergey
AU - Fedorov, Vadim V.
AU - Fedorov, Maxim V
AU - Popov, Petr A.
AU - Popov, Petr
PY - 2020
DA - 2020/03/09
PB - American Chemical Society (ACS)
SP - 5150-5159
IS - 10
VL - 5
PMID - 32201802
SN - 2470-1343
ER -
Cite this
BibTex (up to 50 authors)
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@article{2020_Karlov,
author = {Dmitry S Karlov and Sergey Sosnin and Vadim V. Fedorov and Maxim V Fedorov and Petr A. Popov and Petr Popov},
title = {graphDelta: MPNN Scoring Function for the Affinity Prediction of Protein–Ligand Complexes},
journal = {ACS Omega},
year = {2020},
volume = {5},
publisher = {American Chemical Society (ACS)},
month = {mar},
url = {https://pubs.acs.org/doi/10.1021/acsomega.9b04162},
number = {10},
pages = {5150--5159},
doi = {10.1021/acsomega.9b04162}
}
Cite this
MLA
Copy
Karlov, Dmitry S., et al. “graphDelta: MPNN Scoring Function for the Affinity Prediction of Protein–Ligand Complexes.” ACS Omega, vol. 5, no. 10, Mar. 2020, pp. 5150-5159. https://pubs.acs.org/doi/10.1021/acsomega.9b04162.