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Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning
A common drug repositioning strategy is the re-application of an existing drug to address alternative targets. A crucial aspect to enable such repurposing is that the drug's binding site on the original target is similar to that on the alternative target. Based on the assumption that proteins w...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602481/ https://www.ncbi.nlm.nih.gov/pubmed/31106379 http://dx.doi.org/10.1093/nar/gkz391 |
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author | Ab Ghani, Nur Syatila Ramlan, Effirul Ikhwan Firdaus-Raih, Mohd |
author_facet | Ab Ghani, Nur Syatila Ramlan, Effirul Ikhwan Firdaus-Raih, Mohd |
author_sort | Ab Ghani, Nur Syatila |
collection | PubMed |
description | A common drug repositioning strategy is the re-application of an existing drug to address alternative targets. A crucial aspect to enable such repurposing is that the drug's binding site on the original target is similar to that on the alternative target. Based on the assumption that proteins with similar binding sites may bind to similar drugs, the 3D substructure similarity data can be used to identify similar sites in other proteins that are not known targets. The Drug ReposER (DRug REPOSitioning Exploration Resource) web server is designed to identify potential targets for drug repurposing based on sub-structural similarity to the binding interfaces of known drug binding sites. The application has pre-computed amino acid arrangements from protein structures in the Protein Data Bank that are similar to the 3D arrangements of known drug binding sites thus allowing users to explore them as alternative targets. Users can annotate new structures for sites that are similarly arranged to the residues found in known drug binding interfaces. The search results are presented as mappings of matched sidechain superpositions. The results of the searches can be visualized using an integrated NGL viewer. The Drug ReposER server has no access restrictions and is available at http://mfrlab.org/drugreposer/. |
format | Online Article Text |
id | pubmed-6602481 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-66024812019-07-05 Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning Ab Ghani, Nur Syatila Ramlan, Effirul Ikhwan Firdaus-Raih, Mohd Nucleic Acids Res Web Server Issue A common drug repositioning strategy is the re-application of an existing drug to address alternative targets. A crucial aspect to enable such repurposing is that the drug's binding site on the original target is similar to that on the alternative target. Based on the assumption that proteins with similar binding sites may bind to similar drugs, the 3D substructure similarity data can be used to identify similar sites in other proteins that are not known targets. The Drug ReposER (DRug REPOSitioning Exploration Resource) web server is designed to identify potential targets for drug repurposing based on sub-structural similarity to the binding interfaces of known drug binding sites. The application has pre-computed amino acid arrangements from protein structures in the Protein Data Bank that are similar to the 3D arrangements of known drug binding sites thus allowing users to explore them as alternative targets. Users can annotate new structures for sites that are similarly arranged to the residues found in known drug binding interfaces. The search results are presented as mappings of matched sidechain superpositions. The results of the searches can be visualized using an integrated NGL viewer. The Drug ReposER server has no access restrictions and is available at http://mfrlab.org/drugreposer/. Oxford University Press 2019-07-02 2019-05-20 /pmc/articles/PMC6602481/ /pubmed/31106379 http://dx.doi.org/10.1093/nar/gkz391 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Web Server Issue Ab Ghani, Nur Syatila Ramlan, Effirul Ikhwan Firdaus-Raih, Mohd Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning |
title | Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning |
title_full | Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning |
title_fullStr | Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning |
title_full_unstemmed | Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning |
title_short | Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning |
title_sort | drug reposer: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning |
topic | Web Server Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602481/ https://www.ncbi.nlm.nih.gov/pubmed/31106379 http://dx.doi.org/10.1093/nar/gkz391 |
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