Cargando…
UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network
The in-depth study of protein–protein interactions (PPIs) is of key importance for understanding how cells operate. Therefore, in the past few years, many experimental as well as computational approaches have been developed for the identification and discovery of such interactions. Here, we present...
Autores principales: | , , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7671407/ https://www.ncbi.nlm.nih.gov/pubmed/33575553 http://dx.doi.org/10.1093/nargab/lqaa005 |
_version_ | 1783610923283382272 |
---|---|
author | Theodosiou, Theodosios Papanikolaou, Nikolaos Savvaki, Maria Bonetto, Giulia Maxouri, Stella Fakoureli, Eirini Eliopoulos, Aristides G Tavernarakis, Nektarios Amoutzias, Grigoris D Pavlopoulos, Georgios A Aivaliotis, Michalis Nikoletopoulou, Vasiliki Tzamarias, Dimitris Karagogeos, Domna Iliopoulos, Ioannis |
author_facet | Theodosiou, Theodosios Papanikolaou, Nikolaos Savvaki, Maria Bonetto, Giulia Maxouri, Stella Fakoureli, Eirini Eliopoulos, Aristides G Tavernarakis, Nektarios Amoutzias, Grigoris D Pavlopoulos, Georgios A Aivaliotis, Michalis Nikoletopoulou, Vasiliki Tzamarias, Dimitris Karagogeos, Domna Iliopoulos, Ioannis |
author_sort | Theodosiou, Theodosios |
collection | PubMed |
description | The in-depth study of protein–protein interactions (PPIs) is of key importance for understanding how cells operate. Therefore, in the past few years, many experimental as well as computational approaches have been developed for the identification and discovery of such interactions. Here, we present UniReD, a user-friendly, computational prediction tool which analyses biomedical literature in order to extract known protein associations and suggest undocumented ones. As a proof of concept, we demonstrate its usefulness by experimentally validating six predicted interactions and by benchmarking it against public databases of experimentally validated PPIs succeeding a high coverage. We believe that UniReD can become an important and intuitive resource for experimental biologists in their quest for finding novel associations within a protein network and a useful tool to complement experimental approaches (e.g. mass spectrometry) by producing sorted lists of candidate proteins for further experimental validation. UniReD is available at http://bioinformatics.med.uoc.gr/unired/ |
format | Online Article Text |
id | pubmed-7671407 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-76714072021-02-10 UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network Theodosiou, Theodosios Papanikolaou, Nikolaos Savvaki, Maria Bonetto, Giulia Maxouri, Stella Fakoureli, Eirini Eliopoulos, Aristides G Tavernarakis, Nektarios Amoutzias, Grigoris D Pavlopoulos, Georgios A Aivaliotis, Michalis Nikoletopoulou, Vasiliki Tzamarias, Dimitris Karagogeos, Domna Iliopoulos, Ioannis NAR Genom Bioinform Methart The in-depth study of protein–protein interactions (PPIs) is of key importance for understanding how cells operate. Therefore, in the past few years, many experimental as well as computational approaches have been developed for the identification and discovery of such interactions. Here, we present UniReD, a user-friendly, computational prediction tool which analyses biomedical literature in order to extract known protein associations and suggest undocumented ones. As a proof of concept, we demonstrate its usefulness by experimentally validating six predicted interactions and by benchmarking it against public databases of experimentally validated PPIs succeeding a high coverage. We believe that UniReD can become an important and intuitive resource for experimental biologists in their quest for finding novel associations within a protein network and a useful tool to complement experimental approaches (e.g. mass spectrometry) by producing sorted lists of candidate proteins for further experimental validation. UniReD is available at http://bioinformatics.med.uoc.gr/unired/ Oxford University Press 2020-02-11 /pmc/articles/PMC7671407/ /pubmed/33575553 http://dx.doi.org/10.1093/nargab/lqaa005 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. 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 | Methart Theodosiou, Theodosios Papanikolaou, Nikolaos Savvaki, Maria Bonetto, Giulia Maxouri, Stella Fakoureli, Eirini Eliopoulos, Aristides G Tavernarakis, Nektarios Amoutzias, Grigoris D Pavlopoulos, Georgios A Aivaliotis, Michalis Nikoletopoulou, Vasiliki Tzamarias, Dimitris Karagogeos, Domna Iliopoulos, Ioannis UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network |
title | UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network |
title_full | UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network |
title_fullStr | UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network |
title_full_unstemmed | UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network |
title_short | UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network |
title_sort | uniprot-related documents (unired): assisting wet lab biologists in their quest on finding novel counterparts in a protein network |
topic | Methart |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7671407/ https://www.ncbi.nlm.nih.gov/pubmed/33575553 http://dx.doi.org/10.1093/nargab/lqaa005 |
work_keys_str_mv | AT theodosioutheodosios uniprotrelateddocumentsuniredassistingwetlabbiologistsintheirquestonfindingnovelcounterpartsinaproteinnetwork AT papanikolaounikolaos uniprotrelateddocumentsuniredassistingwetlabbiologistsintheirquestonfindingnovelcounterpartsinaproteinnetwork AT savvakimaria uniprotrelateddocumentsuniredassistingwetlabbiologistsintheirquestonfindingnovelcounterpartsinaproteinnetwork AT bonettogiulia uniprotrelateddocumentsuniredassistingwetlabbiologistsintheirquestonfindingnovelcounterpartsinaproteinnetwork AT maxouristella uniprotrelateddocumentsuniredassistingwetlabbiologistsintheirquestonfindingnovelcounterpartsinaproteinnetwork AT fakourelieirini uniprotrelateddocumentsuniredassistingwetlabbiologistsintheirquestonfindingnovelcounterpartsinaproteinnetwork AT eliopoulosaristidesg uniprotrelateddocumentsuniredassistingwetlabbiologistsintheirquestonfindingnovelcounterpartsinaproteinnetwork AT tavernarakisnektarios uniprotrelateddocumentsuniredassistingwetlabbiologistsintheirquestonfindingnovelcounterpartsinaproteinnetwork AT amoutziasgrigorisd uniprotrelateddocumentsuniredassistingwetlabbiologistsintheirquestonfindingnovelcounterpartsinaproteinnetwork AT pavlopoulosgeorgiosa uniprotrelateddocumentsuniredassistingwetlabbiologistsintheirquestonfindingnovelcounterpartsinaproteinnetwork AT aivaliotismichalis uniprotrelateddocumentsuniredassistingwetlabbiologistsintheirquestonfindingnovelcounterpartsinaproteinnetwork AT nikoletopoulouvasiliki uniprotrelateddocumentsuniredassistingwetlabbiologistsintheirquestonfindingnovelcounterpartsinaproteinnetwork AT tzamariasdimitris uniprotrelateddocumentsuniredassistingwetlabbiologistsintheirquestonfindingnovelcounterpartsinaproteinnetwork AT karagogeosdomna uniprotrelateddocumentsuniredassistingwetlabbiologistsintheirquestonfindingnovelcounterpartsinaproteinnetwork AT iliopoulosioannis uniprotrelateddocumentsuniredassistingwetlabbiologistsintheirquestonfindingnovelcounterpartsinaproteinnetwork |