RNA structure: advances and assessment of 3D structure prediction
Biological functions of RNA molecules are dependent upon sustained specific three-
dimensional (3D) structures of RNA, with or without the help of proteins. Understanding of …
dimensional (3D) structures of RNA, with or without the help of proteins. Understanding of …
RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools
Significant improvements have been made in the efficiency and accuracy of RNA 3D
structure prediction methods during the succeeding challenges of RNA-Puzzles, a …
structure prediction methods during the succeeding challenges of RNA-Puzzles, a …
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction
JA Cruz, MF Blanchet, M Boniecki, JM Bujnicki… - Rna, 2012 - rnajournal.cshlp.org
We report the results of a first, collective, blind experiment in RNA three-dimensional (3D)
structure prediction, encompassing three prediction puzzles. The goals are to assess the …
structure prediction, encompassing three prediction puzzles. The goals are to assess the …
Automated RNA 3D structure prediction with RNAComposer
M Biesiada, KJ Purzycka, M Szachniuk… - … : Methods and Protocols, 2016 - Springer
RNAs adopt specific structures to perform their activities and these are critical to virtually all
RNA-mediated processes. Because of difficulties in experimentally assessing structures of …
RNA-mediated processes. Because of difficulties in experimentally assessing structures of …
Computational approaches to 3D modeling of RNA
C Laing, T Schlick - Journal of Physics: Condensed Matter, 2010 - iopscience.iop.org
Many exciting discoveries have recently revealed the versatility of RNA and its importance in
a variety of functions within the cell. Since the structural features of RNA are of major …
a variety of functions within the cell. Since the structural features of RNA are of major …
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures
Z Miao, RW Adamiak, MF Blanchet, M Boniecki… - Rna, 2015 - rnajournal.cshlp.org
This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment
in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10 …
in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10 …
iFoldRNA v2: folding RNA with constraints
A Krokhotin, K Houlihan, NV Dokholyan - Bioinformatics, 2015 - academic.oup.com
A key to understanding RNA function is to uncover its complex 3D structure. Experimental
methods used for determining RNA 3D structures are technologically challenging and …
methods used for determining RNA 3D structures are technologically challenging and …
Automated 3D structure composition for large RNAs
Understanding the numerous functions that RNAs play in living cells depends critically on
knowledge of their three-dimensional structure. Due to the difficulties in experimentally …
knowledge of their three-dimensional structure. Due to the difficulties in experimentally …
Analysis of four-way junctions in RNA structures
C Laing, T Schlick - Journal of molecular biology, 2009 - Elsevier
RNA secondary structures can be divided into helical regions composed of canonical
Watson–Crick and related base pairs, as well as single-stranded regions such as hairpin …
Watson–Crick and related base pairs, as well as single-stranded regions such as hairpin …