Cargando…

Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best

Algorithmic prediction of RNA secondary structure has been an area of active inquiry since the 1970s. Despite many innovations since then, our best techniques are not yet perfect. The workhorses of the RNA secondary structure prediction engine are recursions first described by Zuker and Stiegler in...

Descripción completa

Detalles Bibliográficos
Autores principales:	Ward, Max, Datta, Amitava, Wise, Michael, Mathews, David H.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2017
Materias:	RNA
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737859/ https://www.ncbi.nlm.nih.gov/pubmed/28586479 http://dx.doi.org/10.1093/nar/gkx512

Ejemplares similares

Deep learning models for RNA secondary structure prediction (probably) do not generalize across families
por: Szikszai, Marcell, et al.
Publicado: (2022)

Dynalign II: common secondary structure prediction for RNA homologs with domain insertions
por: Fu, Yinghan, et al.
Publicado: (2014)

When the Best Pandemic Models are the Simplest
por: Jahedi, Sana, et al.
Publicado: (2020)

McGenus: a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots
por: Bon, Michaël, et al.
Publicado: (2013)

A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
por: Lu, Zhi John, et al.
Publicado: (2006)

Sequence–structure relationships in RNA loops: establishing the basis for loop homology modeling
por: Schudoma, Christian, et al.
Publicado: (2010)

Pan-eukaryote ITS2 homologies revealed by RNA secondary structure
por: Coleman, Annette W.
Publicado: (2007)

A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction
por: Zuber, Jeffrey, et al.
Publicado: (2017)

Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin
por: Zhuang, Zhuoyun, et al.
Publicado: (2007)

Overcrowding estimation in the emergency department: is the simplest score the best?
por: Winkin, V, et al.
Publicado: (2013)

The terminal loop region controls microRNA processing by Drosha and Dicer
por: Zhang, Xiaoxiao, et al.
Publicado: (2010)

Modeling RNA secondary structure folding ensembles using SHAPE mapping data
por: Spasic, Aleksandar, et al.
Publicado: (2018)

Controlled interplay between trigger loop and Gre factor in the RNA polymerase active centre
por: Roghanian, Mohammad, et al.
Publicado: (2011)

Stem–loop structures can effectively substitute for an RNA pseudoknot in −1 ribosomal frameshifting
por: Yu, Chien-Hung, et al.
Publicado: (2011)

tRNA anticodon loop modifications ensure protein homeostasis and cell morphogenesis in yeast
por: Klassen, Roland, et al.
Publicado: (2016)

Additional roles of a peripheral loop–loop interaction in the Neurospora VS ribozyme
por: DeAbreu, Diane M., et al.
Publicado: (2011)

Kluyveromyces lactis γ-toxin, a ribonuclease that recognizes the anticodon stem loop of tRNA
por: Lu, Jian, et al.
Publicado: (2008)

An in vitro-selected RNA receptor for the GAAC loop: modular receptor for non–GNRA-type tetraloop
por: Ishikawa, Junya, et al.
Publicado: (2013)

Two-dimensional combinatorial screening and the RNA Privileged Space Predictor program efficiently identify aminoglycoside–RNA hairpin loop interactions
por: Paul, Dustin J., et al.
Publicado: (2009)

Computing folding pathways between RNA secondary structures
por: Dotu, Ivan, et al.
Publicado: (2010)

Synthesis and investigation of the 5-formylcytidine modified, anticodon stem and loop of the human mitochondrial tRNA(Met)
por: Lusic, Hrvoje, et al.
Publicado: (2008)

Stepwise assembly of multiple Lin28 proteins on the terminal loop of let-7 miRNA precursors
por: Desjardins, Alexandre, et al.
Publicado: (2014)

Loop-miRs: active microRNAs generated from single-stranded loop regions
por: Winter, Julia, et al.
Publicado: (2013)

Stabilization of SMAR1 mRNA by PGA2 involves a stem–loop structure in the 5′ UTR
por: Pavithra, Lakshminarasimhan, et al.
Publicado: (2007)

C to U editing at position 32 of the anticodon loop precedes tRNA 5′ leader removal in trypanosomatids
por: Gaston, Kirk W., et al.
Publicado: (2007)

Aminoglycoside binding to the HIV-1 RNA dimerization initiation site: thermodynamics and effect on the kissing-loop to duplex conversion
por: Bernacchi, Serena, et al.
Publicado: (2007)

Cleavage of the sarcin–ricin loop of 23S rRNA differentially affects EF-G and EF-Tu binding
por: García-Ortega, Lucía, et al.
Publicado: (2010)

Mutational analysis of a Dcp2-binding element reveals general enhancement of decapping by 5′-end stem-loop structures
por: Li, You, et al.
Publicado: (2009)

Tfold: efficient in silico prediction of non-coding RNA secondary structures
por: Engelen, Stéfan, et al.
Publicado: (2010)

A unique conformation of the anticodon stem-loop is associated with the capacity of tRNA(f)(Met) to initiate protein synthesis
por: Barraud, Pierre, et al.
Publicado: (2008)

The conserved 5′ apical hairpin stem loops of bamboo mosaic virus and its satellite RNA contribute to replication competence
por: Chen, Hsin-Chuan, et al.
Publicado: (2012)

Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark
por: Corley, Meredith, et al.
Publicado: (2015)

RNA secondary structure regulates the translation of sxy and competence development in Haemophilus influenzae
por: Cameron, Andrew D.S., et al.
Publicado: (2008)

Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment
por: Zhong, Cuncong, et al.
Publicado: (2012)

Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs
por: Contrant, Maud, et al.
Publicado: (2014)

Attenuation of loop-receptor interactions with pseudoknot formation
por: Afonin, Kirill A., et al.
Publicado: (2012)

In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5′ splice sites
por: Sahashi, Kentaro, et al.
Publicado: (2007)

A cis-encoded sRNA, Hfq and mRNA secondary structure act independently to suppress IS200 transposition
por: Ellis, Michael J., et al.
Publicado: (2015)

Structure–function analysis of the ribozymes of chrysanthemum chlorotic mottle viroid: a loop–loop interaction motif conserved in most natural hammerheads
por: Dufour, David, et al.
Publicado: (2009)

RNA secondary structure of the feline immunodeficiency virus 5′UTR and Gag coding region
por: James, Laurie, et al.
Publicado: (2008)

Cannot write session to /tmp/vufind_sessions/sess_pg76l5la1bo3e09pajnjfliqn7