ModeRNA is a program for comparative modeling of RNA 3D structures. It uses a pairwise sequence alignment and a structural template to generate 3D structural models of the target RNA sequences via either fully-automated or script-based approaches. ModeRNA is capable of handling 115 different nucleotide modifications and can also bridge gaps using fragments derived from an extensive fragment library. Apart from that, ModeRNA offers a multitude of functions for examining and modifying RNA structure files.
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