In this unit, protocols are provided for predicting RNA secondary structure with the user-friendly RNAstructure desktop computer program and the RNAstructure Web server. The minimum free energy structure and a set of suboptimal structures with similar free energies are predicted. Prediction of high-affinity oligonucleotide binding sites to a structured RNA target is also presented. © 2016 by John Wiley & Sons, Inc.
Keywords: RNA folding; RNA secondary structure prediction; binding affinity; free energy minimization; partition function; thermodynamics.
Copyright © 2016 John Wiley & Sons, Inc.