About: ToGo-WF: prediction of RNA tertiary structures and RNA–RNA/protein interactions using the KNIME workflow

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About: ToGo-WF: prediction of RNA tertiary structures and RNA–RNA/protein interactions using the KNIME workflow Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	ToGo-WF: prediction of RNA tertiary structures and RNA–RNA/protein interactions using the KNIME workflow
Creator	Amemiya, Takayuki Fukui, Kazuhiko Horimoto, Katsuhisa Yabuki, Yukimitsu Yamasaki, Satoshi
topic	covid:33171bbcbaa480db4833339e06737b2631c6756f#this
source	Medline; PMC
abstract	Recent progress in molecular biology has revealed that many non-coding RNAs regulate gene expression or catalyze biochemical reactions in tumors, viruses and several other diseases. The tertiary structure of RNA molecules and RNA–RNA/protein interaction sites are of increasing importance as potential targets for new medicines that treat a broad array of human diseases. Current RNA drugs are split into two groups: antisense RNA molecules and aptamers. In this report, we present a novel workflow to predict RNA tertiary structures and RNA–RNA/protein interactions using the KNIME environment, which enabled us to assemble a combination of RNA-related analytical tools and databases. In this study, three analytical workflows for comprehensive structural analysis of RNA are introduced: (1) prediction of the tertiary structure of RNA; (2) prediction of the structure of RNA–RNA complexes and analysis of their interactions; and (3) prediction of the structure of RNA–protein complexes and analysis of their interactions. In an RNA–protein case study, we modeled the tertiary structure of pegaptanib, an aptamer drug, and performed docking calculations of the pegaptanib-vascular endothelial growth factor complex using a fragment of the interaction site of the aptamer. We also present molecular dynamics simulations of the RNA–protein complex to evaluate the affinity of the complex by mutating bases at the interaction interface. The results provide valuable information for designing novel features of aptamer-protein complexes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10822-019-00195-y) contains supplementary material, which is available to authorized users.
has issue date	2019-03-06(xsd:dateTime)
bibo:doi	10.1007/s10822-019-00195-y
bibo:pmid	30840170
has license	no-cc
sha1sum (hex)	33171bbcbaa480db4833339e06737b2631c6756f
schema:url	https://doi.org/10.1007/s10822-019-00195-y
resource representing a document's title	ToGo-WF: prediction of RNA tertiary structures and RNA–RNA/protein interactions using the KNIME workflow
has PubMed Central identifier	PMC7088279
has PubMed identifier	30840170
schema:publication	J Comput Aided Mol Des
resource representing a document's body	covid:33171bbcbaa480db4833339e06737b2631c6756f#body_text
is http://vocab.deri.ie/void#inDataset of	https://covidontheweb.inria.fr:4443/about/id/http/ns.inria.fr/covid19/33171bbcbaa480db4833339e06737b2631c6756f
is schema:about of	named entity 'PREDICT' named entity 'AFFINITY' named entity 'TREAT' named entity 'ENVIRONMENT' named entity 'MEDICINES' »more»

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