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

Predicting structure and stability for RNA complexes with intermolecular loop-loop base-pairing

(2014) S. Cao et al.   RNA

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

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

RNAstructure: web servers for RNA secondary structure prediction and analysis

(2013) Stanislav Bellaousov et al.   NUCLEIC ACIDS RESEARCH

Kinetic Mechanism of Conformational Switch between Bistable RNA Hairpins

(2012) Xiaojun Xu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal

(2011) S. Cao et al.   RNA

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

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

Atomic accuracy in predicting and designing noncanonical RNA structure

(2010) Rhiju Das et al.   NATURE METHODS

On the significance of an RNA tertiary structure prediction

(2010) C. E. Hajdin et al.   RNA

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

CENTROIDFOLD: a web server for RNA secondary structure prediction

(2009) K. Sato et al.   NUCLEIC ACIDS RESEARCH

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

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

Predicting structures and stabilities for H-type pseudoknots with interhelix loops

(2009) S. Cao et al.   RNA

Improved free energy parameters for RNA pseudoknotted secondary structure prediction

(2009) M. S. Andronescu et al.   RNA

iFoldRNA: three-dimensional RNA structure prediction and folding

(2008) Shantanu Sharma et al.   BIOINFORMATICS

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

Discrete state model and accurate estimation of loop entropy of RNA secondary structures

(2008) Jian Zhang et al.   JOURNAL OF CHEMICAL PHYSICS

Relative Stability of Helices Determines the Folding Landscape of Adenine Riboswitch Aptamers

(2008) Jong-Chin Lin 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

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

(2008) F. Ding et al.   RNA