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10.1371/journal.pcbi.1008387 http://scihub22266oqcxt.onion/10.1371/journal.pcbi.1008387 33125376!7657543!33125376     free     free     free Deprecated: Implicit conversion from float 213.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 213.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534       PLoS+Comput+Biol 2020 ; 16 (10): e1008387 Nephropedia Template TP {{tp|p=33125376|t=2020. RNA structure prediction using positive and negative evolutionary information |pdf=|usr=}}{{33125376}} gab.com Text RNA structure prediction using positive and negative evolutionary information JO: PLoS Comput Biol http://www.kidney.de/pget.php?&tw=1&pmid=33125376 #FOAvip Knowing the structure of conserved structural RNAs is important to elucidate their function and mechanism of action. However, predicting a conserved RNA structure remains unreliable, even when using a combination of thermodynamic stability and evolutionary covariation information. Here we present a method to predict a conserved RNA structure that combines the following three features. First, it uses significant covariation due to RNA structure and removes spurious covariation due to phylogeny. Second, it uses negative evolutionary information: basepairs that have variation but no significant covariation are prevented from occurring. Lastly, it uses a battery of probabilistic folding algorithms that incorporate all positive covariation into one structure. The method, named CaCoFold (Cascade variation/covariation Constrained Folding algorithm), predicts a nested structure guided by a maximal subset of positive basepairs, and recursively incorporates all remaining positive basepairs into alternative helices. The alternative helices can be compatible with the nested structure such as pseudoknots, or overlapping such as competing structures, base triplets, or other 3D non-antiparallel interactions. We present evidence that CaCoFold predictions are consistent with structures modeled from crystallography. Twit Text FOAVip RNA structure prediction using positive and negative evolutionary information ????PLoS Comput Biol http://www.kidney.de/pget.php?&tw=1&pmid=33125376 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=33125376 #FOAvip English Wikipedia <ref>{{Cite pmid|33125376}}</ref> RNA structure prediction using positive and negative evolutionary information #MMPMID33125376 Rivas E PLoS Comput Biol 2020[Oct]; 16 (10): e1008387 PMID33125376show ga Knowing the structure of conserved structural RNAs is important to elucidate their function and mechanism of action. However, predicting a conserved RNA structure remains unreliable, even when using a combination of thermodynamic stability and evolutionary covariation information. Here we present a method to predict a conserved RNA structure that combines the following three features. First, it uses significant covariation due to RNA structure and removes spurious covariation due to phylogeny. Second, it uses negative evolutionary information: basepairs that have variation but no significant covariation are prevented from occurring. Lastly, it uses a battery of probabilistic folding algorithms that incorporate all positive covariation into one structure. The method, named CaCoFold (Cascade variation/covariation Constrained Folding algorithm), predicts a nested structure guided by a maximal subset of positive basepairs, and recursively incorporates all remaining positive basepairs into alternative helices. The alternative helices can be compatible with the nested structure such as pseudoknots, or overlapping such as competing structures, base triplets, or other 3D non-antiparallel interactions. We present evidence that CaCoFold predictions are consistent with structures modeled from crystallography. |*RNA/chemistry/genetics/metabolism[MESH] |Algorithms[MESH] |Computational Biology[MESH] |Evolution, Molecular[MESH] |Models, Molecular[MESH] |Nucleic Acid Conformation[MESH] |Sequence Alignment/*methods[MESH] |Sequence Analysis, RNA/*methods[MESH]RNA structure prediction using positive and negative evolutionary info(epmc).pdf DeepDyve Pubget Overpricing