ModeRNA is a tool for comparative modeling of RNA structures. As an input it takes a known RNA structure to be used as a template, and an alignment between the target sequence to be modeled and the template sequence. Then, it carries out a series of operations such as copying the unchanged parts from the template structure to the template structure being modeled, and substitution of changed parts, including individual nucleotides and insertions and deletions.
Insertions and deletions are modeled by the process of fragment replacement, using shorts fragments from known RNA structures. Fragments are selected based on the criteria of spatial compatibility with the rest of the molecule (no physical energy function is used). The models may exhibit minor steric problems, and need to be energy-minimized before further application. Conceptually, ModeRNA is similar to very successful programs for protein structure modeling such as SwissModel or MODELLER. Finally, ModeRNA is capable of modeling posttranscriptional modifications, in which it is unique among feature RNA modeling programs.
ModeRNA has a Python scripting interface and is freely available (GPL) for Linux, Windows, and MaxOS/X at http://iimcb.genesilico.pl/moderna/ .
Rother M, Rother K, Puton T, Bujnicki JM. ModeRNA: a tool for comparative modeling of RNA 3D structure. Nucleic Acids Research, 2011 (in press).
(c) 2011 Magdalena Rother, Kristian Rother, Tomasz Puton, and Janusz M. Bujnicki
