Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure p

Background: A detailed understanding of an RNA's correct secondary and tertiary structure is crucial to understanding its function and mechanism in the cell. Free energy minimization with energy parameters based on the nearest-neighbor model and comparative analysis are the primary methods for predicting an RNA's secondary structure from its sequence. Version 3.1 of Mfold has been available since 1999. This version contains an expanded sequence dependence of energy parameters and the ability to incorporate coaxial stacking into free energy calculations. We test Mfold 3.1 by performing the largest and most phylogenetically diverse comparison of rRNA and tRNA structures predicted by comparative analysis and Mfold, and we use the results of our tests

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Kishore J. Doshi, Jamie J. Cannone, Christian W. Cobaugh, Robin Ray Gutell
• Keywords: BMCBI 2004, Comparative Analysis, Energy Parameters, Free Energy