Cargando…

AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses

RNA is considered as an attractive target for new small molecule drugs. Designing active compounds can be facilitated by computational modeling. Most of the available tools developed for these prediction purposes, such as molecular docking or scoring functions, are parametrized for protein targets....

Descripción completa

Detalles Bibliográficos
Autores principales: Stefaniak, Filip, Bujnicki, Janusz M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7877745/
https://www.ncbi.nlm.nih.gov/pubmed/33524009
http://dx.doi.org/10.1371/journal.pcbi.1008309
_version_ 1783650229428420608
author Stefaniak, Filip
Bujnicki, Janusz M.
author_facet Stefaniak, Filip
Bujnicki, Janusz M.
author_sort Stefaniak, Filip
collection PubMed
description RNA is considered as an attractive target for new small molecule drugs. Designing active compounds can be facilitated by computational modeling. Most of the available tools developed for these prediction purposes, such as molecular docking or scoring functions, are parametrized for protein targets. The performance of these methods, when applied to RNA-ligand systems, is insufficient. To overcome these problems, we developed AnnapuRNA, a new knowledge-based scoring function designed to evaluate RNA-ligand complex structures, generated by any computational docking method. We also evaluated three main factors that may influence the structure prediction, i.e., the starting conformer of a ligand, the docking program, and the scoring function used. We applied the AnnapuRNA method for a post-hoc study of the recently published structures of the FMN riboswitch. Software is available at https://github.com/filipspl/AnnapuRNA.
format Online
Article
Text
id pubmed-7877745
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-78777452021-02-19 AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses Stefaniak, Filip Bujnicki, Janusz M. PLoS Comput Biol Research Article RNA is considered as an attractive target for new small molecule drugs. Designing active compounds can be facilitated by computational modeling. Most of the available tools developed for these prediction purposes, such as molecular docking or scoring functions, are parametrized for protein targets. The performance of these methods, when applied to RNA-ligand systems, is insufficient. To overcome these problems, we developed AnnapuRNA, a new knowledge-based scoring function designed to evaluate RNA-ligand complex structures, generated by any computational docking method. We also evaluated three main factors that may influence the structure prediction, i.e., the starting conformer of a ligand, the docking program, and the scoring function used. We applied the AnnapuRNA method for a post-hoc study of the recently published structures of the FMN riboswitch. Software is available at https://github.com/filipspl/AnnapuRNA. Public Library of Science 2021-02-01 /pmc/articles/PMC7877745/ /pubmed/33524009 http://dx.doi.org/10.1371/journal.pcbi.1008309 Text en © 2021 Stefaniak, Bujnicki http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Stefaniak, Filip
Bujnicki, Janusz M.
AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses
title AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses
title_full AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses
title_fullStr AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses
title_full_unstemmed AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses
title_short AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses
title_sort annapurna: a scoring function for predicting rna-small molecule binding poses
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7877745/
https://www.ncbi.nlm.nih.gov/pubmed/33524009
http://dx.doi.org/10.1371/journal.pcbi.1008309
work_keys_str_mv AT stefaniakfilip annapurnaascoringfunctionforpredictingrnasmallmoleculebindingposes
AT bujnickijanuszm annapurnaascoringfunctionforpredictingrnasmallmoleculebindingposes