The role of nucleobase interactions in RNA structure and dynamics

A Decade of Riboswitches

(2013) Alexander Serganov et al.   CELL

Computer Folding of RNA Tetraloops? Are We There Yet?

(2013) Petra Kührová et al.   Journal of Chemical Theory and Computation

Coarse-Grained Model for Predicting RNA Folding Thermodynamics

(2013) Natalia A. Denesyuk et al.   JOURNAL OF PHYSICAL CHEMISTRY B

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

(2013) A. A. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

(2013) A. I. Petrov et al.   RNA

Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch

(2013) F. Di Palma et al.   RNA

Distribution of Reciprocal of Interatomic Distances: A Fast Structural Metric

(2012) Ting Zhou et al.   Journal of Chemical Theory and Computation

Simple few-state models reveal hidden complexity in protein folding

(2012) K. A. Beauchamp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

(2012) J. A. Cruz et al.   RNA

A simple and efficient statistical potential for scoring ensembles of protein structures

(2012) Pilar Cossio et al.   Scientific Reports

All-atom knowledge-based potential for RNA structure prediction and assessment

(2011) Emidio Capriotti et al.   BIOINFORMATICS

Physics-Based De Novo Prediction of RNA 3D Structures

(2011) Song Cao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

(2011) Pilar Cossio et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation

(2011) J. Bernauer et al.   RNA

Atomic accuracy in predicting and designing noncanonical RNA structure

(2010) Rhiju Das et al.   NATURE METHODS

RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment

(2010) Cuncong Zhong et al.   NUCLEIC ACIDS RESEARCH

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

Finding 3D motifs in ribosomal RNA structures

(2009) A. Apostolico et al.   NUCLEIC ACIDS RESEARCH

New metrics for comparing and assessing discrepancies between RNA 3D structures and models

(2009) M. Parisien et al.   RNA

A Probabilistic Model of RNA Conformational Space

(2009) Jes Frellsen et al.   PLoS Computational Biology

The Unfolded Ensemble and Folding Mechanism of the C-Terminal GB1 β-Hairpin

(2008) Massimiliano Bonomi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

(2008) Marc Parisien et al.   NATURE

Nature and magnitude of aromatic stacking of nucleic acid bases

(2008) Jiří Šponer et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

(2008) F. Ding et al.   RNA