The importance of ARG513 as a hydrogen bond anchor to discover COX-2 inhibitors in a virtual screening campaign

Structure-based virtual screening (SBVS) protocols were developed to find cyclooxygenase-2 (COX-2) inhibitors using the Protein-Ligand ANT System (PLANTS) docking software. The directory of useful decoys (DUD) dataset for COX-2 was used to retrospectively validate the protocols; the DUD consists of...

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Detalles Bibliográficos
Autores principales: Yuniarti, Nunung, Ikawati, Zullies, Istyastono, Enade Perdana
Formato: Texto
Lenguaje:English
Publicado: Biomedical Informatics 2011
Materias:
Hypothesis
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3092952/
https://www.ncbi.nlm.nih.gov/pubmed/21572885
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author Yuniarti, Nunung
Ikawati, Zullies
Istyastono, Enade Perdana
author_facet Yuniarti, Nunung
Ikawati, Zullies
Istyastono, Enade Perdana
author_sort Yuniarti, Nunung
collection PubMed
description Structure-based virtual screening (SBVS) protocols were developed to find cyclooxygenase-2 (COX-2) inhibitors using the Protein-Ligand ANT System (PLANTS) docking software. The directory of useful decoys (DUD) dataset for COX-2 was used to retrospectively validate the protocols; the DUD consists of 426 known inhibitors in 13289 decoys. Based on criteria used in the article describing DUD datasets, the default protocol showed poor results. However, having ARG513 as a hydrogen bond anchor increased the quality of the SBVS protocol. The modified protocol showed results that could be well considered, with a maximum enrichment factor (EF(max)) value of 32.2.
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spelling pubmed-30929522011-05-13 The importance of ARG513 as a hydrogen bond anchor to discover COX-2 inhibitors in a virtual screening campaign Yuniarti, Nunung Ikawati, Zullies Istyastono, Enade Perdana Bioinformation Hypothesis Structure-based virtual screening (SBVS) protocols were developed to find cyclooxygenase-2 (COX-2) inhibitors using the Protein-Ligand ANT System (PLANTS) docking software. The directory of useful decoys (DUD) dataset for COX-2 was used to retrospectively validate the protocols; the DUD consists of 426 known inhibitors in 13289 decoys. Based on criteria used in the article describing DUD datasets, the default protocol showed poor results. However, having ARG513 as a hydrogen bond anchor increased the quality of the SBVS protocol. The modified protocol showed results that could be well considered, with a maximum enrichment factor (EF(max)) value of 32.2. Biomedical Informatics 2011-05-07 /pmc/articles/PMC3092952/ /pubmed/21572885 Text en © 2011 Biomedical Informatics This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
spellingShingle Hypothesis
Yuniarti, Nunung
Ikawati, Zullies
Istyastono, Enade Perdana
The importance of ARG513 as a hydrogen bond anchor to discover COX-2 inhibitors in a virtual screening campaign
title The importance of ARG513 as a hydrogen bond anchor to discover COX-2 inhibitors in a virtual screening campaign
title_full The importance of ARG513 as a hydrogen bond anchor to discover COX-2 inhibitors in a virtual screening campaign
title_fullStr The importance of ARG513 as a hydrogen bond anchor to discover COX-2 inhibitors in a virtual screening campaign
title_full_unstemmed The importance of ARG513 as a hydrogen bond anchor to discover COX-2 inhibitors in a virtual screening campaign
title_short The importance of ARG513 as a hydrogen bond anchor to discover COX-2 inhibitors in a virtual screening campaign
title_sort importance of arg513 as a hydrogen bond anchor to discover cox-2 inhibitors in a virtual screening campaign
topic Hypothesis
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3092952/
https://www.ncbi.nlm.nih.gov/pubmed/21572885
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