TY - JOUR
T1 - Improved prediction of RNA tertiary structure with insights into native state dynamics
AU - Bida, John Paul
AU - Maher, L. James
PY - 2012/3
Y1 - 2012/3
N2 - The importance of RNA tertiary structure is evident from the growing number of published high resolution NMR and X-ray crystallographic structures of RNA molecules. These structures provide insights into function and create a knowledge base that is leveraged by programs such as Assemble, ModeRNA, RNABuilder, NAST, FARNA, Mc-Sym, RNA2D3D, and iFoldRNA for tertiary structure prediction and design. While these methods sample native-like RNA structures during simulations, all struggle to capture the native RNA conformation after scoring. We propose RSIM, an improved RNA fragment assembly method that preserves RNA global secondary structure while sampling conformations. This approach enhances the quality of predicted RNA tertiary structure, provides insights into the native state dynamics, and generates a powerful visualization of the RNA conformational space. RSIM is available for download from http://www.github.com/jpbida/rsim. Published by Cold Spring Harbor Laboratory Press.
AB - The importance of RNA tertiary structure is evident from the growing number of published high resolution NMR and X-ray crystallographic structures of RNA molecules. These structures provide insights into function and create a knowledge base that is leveraged by programs such as Assemble, ModeRNA, RNABuilder, NAST, FARNA, Mc-Sym, RNA2D3D, and iFoldRNA for tertiary structure prediction and design. While these methods sample native-like RNA structures during simulations, all struggle to capture the native RNA conformation after scoring. We propose RSIM, an improved RNA fragment assembly method that preserves RNA global secondary structure while sampling conformations. This approach enhances the quality of predicted RNA tertiary structure, provides insights into the native state dynamics, and generates a powerful visualization of the RNA conformational space. RSIM is available for download from http://www.github.com/jpbida/rsim. Published by Cold Spring Harbor Laboratory Press.
KW - Aptamer
KW - Conformation
KW - Monte Carlo
KW - Noncanonical base-pairing
KW - RNA tertiary structure prediction
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U2 - 10.1261/rna.027201.111
DO - 10.1261/rna.027201.111
M3 - Article
C2 - 22279150
AN - SCOPUS:84857412659
SN - 1355-8382
VL - 18
SP - 385
EP - 393
JO - RNA
JF - RNA
IS - 3
ER -