De novo tertiary structure prediction using RNA123—benchmarking and application to Macugen

RNA G-Quadruplexes: G-quadruplexes with “U” Turns

(2012) Tani Agarwal et al.   CURRENT PHARMACEUTICAL DESIGN

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

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

Comprehensive survey and geometric classification of base triples in RNA structures

(2011) Amal S. Abu Almakarem et al.   NUCLEIC ACIDS RESEARCH

RNA Internal Loops with Tandem AG Pairs: The Structure of the 5′GAGU/3′UGAG Loop Can Be Dramatically Different from Others, Including 5′AAGU/3′UGAA

(2010) Nicholas B. Hammond et al.   BIOCHEMISTRY

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

(2010) F. Jossinet et al.   BIOINFORMATICS

Atomic accuracy in predicting and designing noncanonical RNA structure

(2010) Rhiju Das et al.   NATURE METHODS

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

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

(2009) M. A. Jonikas et al.   RNA

iFoldRNA: three-dimensional RNA structure prediction and folding

(2008) Shantanu Sharma et al.   BIOINFORMATICS

Imino proton exchange rates imply an induced-fit binding mechanism for the VEGF165-targeting aptamer, Macugen

(2008) Joon-Hwa Lee et al.   FEBS LETTERS

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

Frameshifting RNA pseudoknots: Structure and mechanism

(2008) David P. Giedroc et al.   VIRUS RESEARCH