Advances and opportunities in RNA structure experimental determination and computational modeling
Beyond transferring genetic information, RNAs are molecules with diverse functions that
include catalyzing biochemical reactions and regulating gene expression. Most of these …
include catalyzing biochemical reactions and regulating gene expression. Most of these …
RNA structural dynamics as captured by molecular simulations: a comprehensive overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
Perspective: Coarse-grained models for biomolecular systems
WG Noid - The Journal of chemical physics, 2013 - pubs.aip.org
By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …
grained (CG) models provide significant computational and conceptual advantages with …
The power of coarse graining in biomolecular simulations
Computational modeling of biological systems is challenging because of the multitude of
spatial and temporal scales involved. Replacing atomistic detail with lower resolution …
spatial and temporal scales involved. Replacing atomistic detail with lower resolution …
FARFAR2: improved de novo rosetta prediction of complex global RNA folds
Predicting RNA three-dimensional structures from sequence could accelerate
understanding of the growing number of RNA molecules being discovered across biology …
understanding of the growing number of RNA molecules being discovered across biology …
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction
RNA molecules play fundamental roles in cellular processes. Their function and interactions
with other biomolecules are dependent on the ability to form complex three-dimensional …
with other biomolecules are dependent on the ability to form complex three-dimensional …
Accurate SHAPE-directed RNA structure determination
KE Deigan, TW Li, DH Mathews… - Proceedings of the …, 2009 - National Acad Sciences
Almost all RNAs can fold to form extensive base-paired secondary structures. Many of these
structures then modulate numerous fundamental elements of gene expression. Deducing …
structures then modulate numerous fundamental elements of gene expression. Deducing …
Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model
We explore in detail the structural, mechanical, and thermodynamic properties of a coarse-
grained model of DNA similar to that recently introduced in a study of DNA nanotweezers …
grained model of DNA similar to that recently introduced in a study of DNA nanotweezers …
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of
RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are …
RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are …
RNA-Puzzles Round V: blind predictions of 23 RNA structures
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of
RNA three-dimensional structure prediction. With agreement from structural biologists, RNA …
RNA three-dimensional structure prediction. With agreement from structural biologists, RNA …