A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

(2017) Zhichao Miao et al.   RNA

Free Energy Landscape of GAGA and UUCG RNA Tetraloops

(2016) Sandro Bottaro et al.   Journal of Physical Chemistry Letters

RNAlien – Unsupervised RNA family model construction

(2016) Florian Eggenhofer et al.   NUCLEIC ACIDS RESEARCH

Structure Prediction of RNA Loops with a Probabilistic Approach

(2016) Jun Li et al.   PLoS Computational Biology

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction

(2015) Michal J. Boniecki et al.   NUCLEIC ACIDS RESEARCH

Predicting RNA 3D structure using a coarse-grain helix-centered model

(2015) Peter Kerpedjiev et al.   RNA

RNA-PuzzlesRound II: assessment of RNA structure prediction programs applied to three large RNA structures

(2015) Zhichao Miao et al.   RNA

Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

(2015) Christina Bergonzo et al.   RNA

A nucleotide-level coarse-grained model of RNA

(2014) Petr Šulc et al.   JOURNAL OF CHEMICAL PHYSICS

A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions

(2014) Adam Liwo et al.   JOURNAL OF MOLECULAR MODELING

Coarse Grained Models Reveal Essential Contributions of Topological Constraints to the Conformational Free Energy of RNA Bulges

(2014) Anthony M. Mustoe et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

(2014) Jiří Šponer et al.   Journal of Physical Chemistry Letters

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

The role of nucleobase interactions in RNA structure and dynamics

(2014) Sandro Bottaro et al.   NUCLEIC ACIDS RESEARCH

Vfold: A Web Server for RNA Structure and Folding Thermodynamics Prediction

(2014) Xiaojun Xu et al.   PLoS One

A Decade of Riboswitches

(2013) Alexander Serganov et al.   CELL

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

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

Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure

(2012) V. Reinharz et al.   BIOINFORMATICS

RNA2D3D: A program for Generating, Viewing, and Comparing 3-Dimensional Models of RNA

(2012) Hugo M. Martinez et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Automated 3D structure composition for large RNAs

(2012) Mariusz Popenda et al.   NUCLEIC ACIDS RESEARCH

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

(2012) J. A. Cruz et al.   RNA

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

(2011) J. Bernauer et al.   RNA

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels

(2010) F. Jossinet et al.   BIOINFORMATICS

Prediction of RNA multiloop and pseudoknot conformations from a lattice-based, coarse-grain tertiary structure model

(2010) Daniel Jost et al.   JOURNAL OF CHEMICAL PHYSICS

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

(2010) Pavel Banáš et al.   Journal of Chemical Theory and Computation

Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures

(2010) Zhen Xia et al.   JOURNAL OF PHYSICAL CHEMISTRY B

HiRE-RNA: A High Resolution Coarse-Grained Energy Model for RNA

(2010) Samuela Pasquali et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Atomic accuracy in predicting and designing noncanonical RNA structure

(2010) Rhiju Das et al.   NATURE METHODS

RNA in evolution

(2010) Niles Lehman   Wiley Interdisciplinary Reviews-RNA

Classification and energetics of the base-phosphate interactions in RNA

(2009) Craig L. Zirbel et al.   NUCLEIC ACIDS RESEARCH

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

(2009) M. A. Jonikas et al.   RNA

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

(2009) M. Parisien et al.   RNA

iFoldRNA: three-dimensional RNA structure prediction and folding

(2008) Shantanu Sharma et al.   BIOINFORMATICS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2008) Marc Parisien et al.   NATURE

RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

(2008) J. S. Richardson et al.   RNA