TBI-p-2014-9

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Titel:
Predicting 3D RNA structure using a coarse-grain helix-centered model

Author(s):
Peter Kerpedjiev, Christian Höner zu Siederdissen, and Ivo L. Hofacker

submitted to:

Abstract:
Motivation: A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy and long running times and either neglect or presume knowledge of the long range interactions which stabilize the tertiary structure. Results: Our coarse-grained, helix-based, tertiary structure model operates with only a few degrees of freedom compared to all-atom models while preserving the ability to sample structures given a secondary structure model. It strikes a balance between the accuracy of an all-atom tertiary structure model and the simplicity and effectiveness of a secondary structure representation. It eases the computational requirements necessary for the prediction of tertiary structure while retaining the ability to generate models as good as or better than the current state of the art prediction tools. Availability: Ernwin is licensed under the GPL-V3 license and available here: http://github.com/pkerpedjiev/ernwin Contact: {pkerp,choener,ivo}@tbi.univie.ac.at

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