Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning

Nur Syatila Ab Ghani, E. Ramlan, Mohd Firdaus-Raih

Research output: Contribution to journalArticle

Abstract

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/.
LanguageEnglish
PagesW350-W356
Number of pages7
JournalNucleic Acids Research
Volume47
Issue numberW1
Early online date20 May 2019
DOIs
Publication statusE-pub ahead of print - 20 May 2019

Fingerprint

Drug Repositioning
Amino Acids
Pharmaceutical Preparations
Binding Sites
Proteins
Databases

Cite this

@article{398e170265824fe79720ed7d2c32508b,
title = "Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning",
abstract = "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/.",
author = "{Ab Ghani}, {Nur Syatila} and E. Ramlan and Mohd Firdaus-Raih",
year = "2019",
month = "5",
day = "20",
doi = "10.1093/nar/gkz391",
language = "English",
volume = "47",
pages = "W350--W356",
journal = "Nucleic Acids Research",
issn = "0305-1048",
number = "W1",

}

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, E.; Firdaus-Raih, Mohd.

In: Nucleic Acids Research, Vol. 47, No. W1, 20.05.2019, p. W350-W356.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning

AU - Ab Ghani, Nur Syatila

AU - Ramlan, E.

AU - Firdaus-Raih, Mohd

PY - 2019/5/20

Y1 - 2019/5/20

N2 - 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/.

AB - 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/.

UR - http://www.scopus.com/inward/record.url?scp=85069237033&partnerID=8YFLogxK

U2 - 10.1093/nar/gkz391

DO - 10.1093/nar/gkz391

M3 - Article

VL - 47

SP - W350-W356

JO - Nucleic Acids Research

T2 - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - W1

ER -