Open Access
Advances and Applications in Bioinformatics and Chemistry, volume 5, issue 1, pages 61-79
Contact-based ligand-clustering approach for the identification of active compounds in virtual screening
Publication type: Journal Article
Publication date: 2012-09-05
Quartile SCImago
Q2
Quartile WOS
—
Impact factor: —
ISSN: 11786949
PubMed ID:
23055752
Biochemistry
Computer Science Applications
Chemistry (miscellaneous)
Biochemistry, Genetics and Molecular Biology (miscellaneous)
Abstract
Evaluation of docking results is one of the most important problems for virtual screening and in silico drug design. Modern approaches for the identification of active compounds in a large data set of docked molecules use energy scoring functions. One of the general and most significant limitations of these methods relates to inaccurate binding energy estimation, which results in false scoring of docked compounds. Automatic analysis of poses using self-organizing maps (AuPosSOM) represents an alternative approach for the evaluation of docking results based on the clustering of compounds by the similarity of their contacts with the receptor. A scoring function was developed for the identification of the active compounds in the AuPosSOM clustered dataset. In addition, the AuPosSOM efficiency for the clustering of compounds and the identification of key contacts considered as important for its activity, were also improved. Benchmark tests for several targets revealed that together with the developed scoring function, AuPosSOM represents a good alternative to the energy-based scoring functions for the evaluation of docking results.
Citations by journals
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1
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International Journal of Molecular Sciences
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International Journal of Molecular Sciences
1 publication, 14.29%
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Frontiers in Physiology
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Frontiers in Physiology
1 publication, 14.29%
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Biochemistry
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Biochemistry
1 publication, 14.29%
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Journal of Physical Chemistry B
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1 publication, 14.29%
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Journal of Chemical Theory and Computation
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1 publication, 14.29%
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Jundishapur Journal of Natural Pharmaceutical Products
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Jundishapur Journal of Natural Pharmaceutical Products, 1, 14.29%
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1 publication, 14.29%
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ACS Biomaterials Science and Engineering
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ACS Biomaterials Science and Engineering
1 publication, 14.29%
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1
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Citations by publishers
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4
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American Chemical Society (ACS)
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American Chemical Society (ACS)
4 publications, 57.14%
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Multidisciplinary Digital Publishing Institute (MDPI)
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Multidisciplinary Digital Publishing Institute (MDPI)
1 publication, 14.29%
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Frontiers Media S.A.
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Frontiers Media S.A.
1 publication, 14.29%
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Kowsar Publishing Company
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Kowsar Publishing Company, 1, 14.29%
Kowsar Publishing Company
1 publication, 14.29%
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4
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- We do not take into account publications that without a DOI.
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- Statistics recalculated weekly.
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Bertho G. et al. Contact-based ligand-clustering approach for the identification of active compounds in virtual screening // Advances and Applications in Bioinformatics and Chemistry. 2012. Vol. 5. No. 1. pp. 61-79.
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Bertho G., Mantsyzov, Bouvier, Evrard Todeschi Contact-based ligand-clustering approach for the identification of active compounds in virtual screening // Advances and Applications in Bioinformatics and Chemistry. 2012. Vol. 5. No. 1. pp. 61-79.
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TY - JOUR
DO - 10.2147/AABC.S30881
UR - https://doi.org/10.2147%2FAABC.S30881
TI - Contact-based ligand-clustering approach for the identification of active compounds in virtual screening
T2 - Advances and Applications in Bioinformatics and Chemistry
AU - Bertho, Gildas
AU - Mantsyzov
AU - Bouvier
AU - Evrard Todeschi
PY - 2012
DA - 2012/09/05 00:00:00
PB - Dove Medical Press
SP - 61-79
IS - 1
VL - 5
PMID - 23055752
SN - 1178-6949
ER -
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BibTex
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@article{2012_Bertho,
author = {Gildas Bertho and Mantsyzov and Bouvier and Evrard Todeschi},
title = {Contact-based ligand-clustering approach for the identification of active compounds in virtual screening},
journal = {Advances and Applications in Bioinformatics and Chemistry},
year = {2012},
volume = {5},
publisher = {Dove Medical Press},
month = {sep},
url = {https://doi.org/10.2147%2FAABC.S30881},
number = {1},
pages = {61--79},
doi = {10.2147/AABC.S30881}
}
Cite this
MLA
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Bertho, Gildas, et al. “Contact-based ligand-clustering approach for the identification of active compounds in virtual screening.” Advances and Applications in Bioinformatics and Chemistry, vol. 5, no. 1, Sep. 2012, pp. 61-79. https://doi.org/10.2147%2FAABC.S30881.
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