RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules

ERD: a fast and reliable tool for RNA design including constraints

(2015) Ali Esmaili-Taheri et al.   BMC BIOINFORMATICS

Sampled ensemble neutrality as a feature to classify potential structured RNAs

(2015) Shermin Pei et al.   BMC GENOMICS

High-Affinity Recognition of HIV-1 Frameshift-Stimulating RNA Alters Frameshifting in Vitro and Interferes with HIV-1 Infectivity

(2014) Leslie O. Ofori et al.   JOURNAL OF MEDICINAL CHEMISTRY

Complete RNA inverse folding: computational design of functional hammerhead ribozymes

(2014) Ivan Dotu et al.   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

RNAfbinv: an interactive Java application for fragment-based design of RNA sequences

(2013) L. Weinbrand et al.   BIOINFORMATICS

A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution

(2013) Vladimir Reinharz et al.   BIOINFORMATICS

RNAiFold: a web server for RNA inverse folding and molecular design

(2013) Juan Antonio Garcia-Martin et al.   NUCLEIC ACIDS RESEARCH

Using RNA inverse folding to identify IRES-like structural subdomains

(2013) Ivan Dotu et al.   RNA Biology

Frnakenstein: multiple target inverse RNA folding

(2012) Rune B Lyngsø et al.   BMC BIOINFORMATICS

RNAiFOLD: A CONSTRAINT PROGRAMMING ALGORITHM FOR RNA INVERSE FOLDING AND MOLECULAR DESIGN

(2012) JUAN ANTONIO GARCIA-MARTIN et al.   Journal of Bioinformatics and Computational Biology

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Nucleic acid sequence design via efficient ensemble defect optimization

(2010) Joseph N. Zadeh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

Strategies for measuring evolutionary conservation of RNA secondary structures

(2008) Andreas R Gruber et al.   BMC BIOINFORMATICS

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH