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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....
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
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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 |
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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 |