Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs

3D RNA and Functional Interactions from Evolutionary Couplings

(2016) Caleb Weinreb et al.   CELL

Critical assessment of methods of protein structure prediction: Progress and new directions in round XI

(2016) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

iFoldRNA v2: folding RNA with constraints: Fig. 1.

(2015) Andrey Krokhotin et al.   BIOINFORMATICS

Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark

(2015) Meredith Corley et al.   NUCLEIC ACIDS RESEARCH

Thermodynamic matchers for the construction of the cuckoo RNA family

(2015) Jan Reinkensmeier et al.   RNA Biology

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

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

Crystal structure and mechanistic investigation of the twister ribozyme

(2014) Yijin Liu et al.   Nature Chemical Biology

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

The Structural Basis of Pathogenic Subgenomic Flavivirus RNA (sfRNA) Production

(2014) E. G. Chapman et al.   SCIENCE

RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs

(2013) Radhakrishnan Sabarinathan et al.   HUMAN MUTATION

TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots

(2012) Matthew G. Seetin et al.   BIOINFORMATICS

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies

(2012) Raheleh Salari et al.   NUCLEIC ACIDS RESEARCH

Automated 3D structure composition for large RNAs

(2012) Mariusz Popenda et al.   NUCLEIC ACIDS RESEARCH

The Protein-Folding Problem, 50 Years On

(2012) K. A. Dill et al.   SCIENCE

A folding algorithm for extended RNA secondary structures

(2011) C. H. zu Siederdissen et al.   BIOINFORMATICS

TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences

(2011) Arif O Harmanci et al.   BMC BIOINFORMATICS

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

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

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

(2011) Magdalena Rother et al.   NUCLEIC ACIDS RESEARCH

The Crystal Structure of the Signal Recognition Particle in Complex with Its Receptor

(2011) S. F. Ataide et al.   SCIENCE

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Fast Flexible Modeling of RNA Structure Using Internal Coordinates

(2010) S. C. Flores et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Atomic accuracy in predicting and designing noncanonical RNA structure

(2010) Rhiju Das et al.   NATURE METHODS

ProbKnot: Fast prediction of RNA secondary structure including pseudoknots

(2010) S. Bellaousov et al.   RNA

Turning limited experimental information into 3D models of RNA

(2010) S. C. Flores et al.   RNA

Disease-Associated Mutations That Alter the RNA Structural Ensemble

(2010) Matthew Halvorsen et al.   PLoS Genetics

Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models

(2009) Magdalena A. Jonikas et al.   BIOINFORMATICS

Native-like RNA Tertiary Structures Using a Sequence-Encoded Cleavage Agent and Refinement by Discrete Molecular Dynamics

(2009) Costin M. Gherghe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

(2009) Douglas H. Turner et al.   NUCLEIC ACIDS RESEARCH

Improved RNA secondary structure prediction by maximizing expected pair accuracy

(2009) Z. J. Lu et al.   RNA

iFoldRNA: three-dimensional RNA structure prediction and folding

(2008) Shantanu Sharma et al.   BIOINFORMATICS

RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

(2008) Mirela Andronescu et al.   BMC BIOINFORMATICS

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

(2008) Marc Parisien et al.   NATURE

The impact of target site accessibility on the design of effective siRNAs

(2008) Hakim Tafer et al.   NATURE BIOTECHNOLOGY

OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics

(2008) Z. J. Lu et al.   NUCLEIC ACIDS RESEARCH