Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction

(2012) Stefan Washietl et al.   NUCLEIC ACIDS RESEARCH

Understanding the Errors of SHAPE-Directed RNA Structure Modeling

(2011) Wipapat Kladwang et al.   BIOCHEMISTRY

Modeling and automation of sequencing-based characterization of RNA structure

(2011) S. Aviran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Correlating SHAPE signatures with three-dimensional RNA structures

(2011) E. Bindewald et al.   RNA

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Advances in RNA structure analysis by chemical probing

(2010) Kevin M Weeks   CURRENT OPINION IN STRUCTURAL BIOLOGY

Evaluation of the information content of RNA structure mapping data for secondary structure prediction

(2010) S. Quarrier et al.   RNA

Architecture and secondary structure of an entire HIV-1 RNA genome

(2009) Joseph M. Watts et al.   NATURE

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

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

Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA

(2009) K. A. Wilkinson et al.   RNA

Beyond energy minimization: approaches to the kinetic folding of RNA

(2008) Christoph Flamm et al.   MONATSHEFTE FUR CHEMIE

Accurate SHAPE-directed RNA structure determination

(2008) K. E. Deigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States

(2008) Kevin A Wilkinson et al.   PLOS BIOLOGY