mqapRNA


RNA 3D models

The SimRNAweb simulations were done as work of the Bujnicki lab members.

Moco motif

The ranking of models is available http://genesilico.pl/mqapRNA/jobs/01f12da9-46c0-47a5-bd95-65ddc4df1401

The Moco RNA motif is a conserved RNA structure that is presumed to be a riboswitch that binds molybdenum cofactor or the related tungsten cofactor. Genetic experiments support the hypothesis that the Moco RNA motif corresponds to a genetic control element that responds to changing concentrations of molybdenum or tungsten cofactor. As these cofactors are not available in purified form, in vitro binding assays cannot be performed. However, the genetic data, complex structure of the RNA and the failure to detect a protein involved in the regulation suggest that the Moco RNA motif corresponds to a class of riboswitches. https://en.wikipedia.org/wiki/Moco_RNA_motif

Downstream peptide

The ranking of models is available http://genesilico.pl/mqapRNA/jobs/5cd59296-184c-4c07-ae85-11609ea383e2

The Downstream-peptide motif refers to a conserved RNA structure identified by bioinformatics in the cyanobacterial genera Synechococcus and Prochlorococcus and one phage that infects such bacteria. It was also detected in marine samples of DNA from uncultivated bacteria, which are presumably other species of cyanobacteria... https://en.wikipedia.org/wiki/Downstream-peptide_motif

YjdF motif

The ranking of models is available http://genesilico.pl/mqapRNA/jobs/70e1e318-b1a1-46a7-bcb7-f945758bf660

The yjdF RNA motif is a conserved RNA structure identified using bioinformatics. Most yjdF RNAs are located in bacteria classified within the phylum Firmicutes. A yjdF RNA is found in the presumed 5' untranslated region (5' UTR) of the yjdF gene in Bacillus subtilis, and almost all yjdF RNAs are found in the 5' UTRs of homologs of this gene. The function of the yjdF gene is unknown, but the protein that it is predicted to encode is classified by the Pfam Database as DUF2992... https://en.wikipedia.org/wiki/YjdF_RNA_motif

The SimRNAweb simulation http://genesilico.pl/SimRNAweb/jobs/UR5_1764_yjdF-dcc0f00f/