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

Identifying novel sequence variants of RNA 3D motifs

(2015) Craig L. Zirbel et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Zhichao Miao et al.   RNA

A nucleotide-level coarse-grained model of RNA

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

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

ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes

(2014) Tomasz Waleń et al.   NUCLEIC ACIDS RESEARCH

Graph-based sampling for approximating global helical topologies of RNA

(2014) N. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational modeling of RNA 3D structures, with the aid of experimental restraints

(2014) Marcin Magnus et al.   RNA Biology

Coarse-Graining Methods for Computational Biology

(2013) Marissa G. Saunders et al.   Annual Review of Biophysics

An Algorithmic Game-Theory Approach for Coarse-Grain Prediction of RNA 3D Structure

(2013) Alexis Lamiable et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

RNA 3D Structure Prediction by Using a Coarse-Grained Model and Experimental Data

(2013) Zhen Xia et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse-Grained Model for Predicting RNA Folding Thermodynamics

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

Solution conformation of adenovirus virus associated RNA-I and its interaction with PKR

(2013) Edis Dzananovic et al.   JOURNAL OF STRUCTURAL BIOLOGY

S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA

(2013) D. Matelska et al.   RNA

Molecular recognition and function of riboswitches

(2012) Alexander Serganov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Modeling and design by hierarchical natural moves

(2012) A. Y. L. Sim 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

ModeRNA server: an online tool for modeling RNA 3D structures

(2011) M. Rother et al.   BIOINFORMATICS

Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints

(2011) Matthew G. Seetin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

RNA and protein 3D structure modeling: similarities and differences

(2011) Kristian Rother et al.   JOURNAL OF MOLECULAR MODELING

Physics-Based De Novo Prediction of RNA 3D Structures

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

Sequence-based identification of 3D structural modules in RNA with RMDetect

(2011) José Almeida Cruz et al.   NATURE METHODS

ModeRNA: a tool for comparative modeling of RNA 3D structure

(2011) Magdalena Rother et al.   NUCLEIC ACIDS RESEARCH

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

(2011) J. Bernauer et al.   RNA

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

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

Nucleases: diversity of structure, function and mechanism

(2010) Wei Yang   QUARTERLY REVIEWS OF BIOPHYSICS

On the significance of an RNA tertiary structure prediction

(2010) C. E. Hajdin et al.   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

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

(2008) Marc Parisien et al.   NATURE

LocalMove: computing on-lattice fits for biopolymers

(2008) Y. Ponty et al.   NUCLEIC ACIDS RESEARCH

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

(2008) F. Ding et al.   RNA