GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization

Abstract

Motivation: Predicting the 3D structure of RNA molecules is a key feature towards predicting their functions. Methods which work at atomic or nucleotide level are not suitable for large molecules. In these cases, coarse-grained prediction methods aim to predict a shape which could be refined later by using more precise methods on smaller parts of the molecule.

Results: We developed a complete method for sampling 3D RNA structure at a coarse-grained model, taking a secondary structure as input. One of the novelties of our method is that a second step extracts two best possible structures close to the native, from a set of possible structures. Although our method benefits from the first version of GARN, some of the main features on GARN2 are very different. GARN2 is much faster than the previous version and than the well-known methods of the state-of-art. Our experiments show that GARN2 can also provide better structures than the other state-of-the-art methods.

Availability and implementation: GARN2 is written in Java. It is freely distributed and available at http://garn.lri.fr/.

Contact: melanie.boudard@lri.fr or johanne.cohen@lri.fr.

Supplementary information: Supplementary data are available at Bioinformatics online.