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Background  Many functional RNA molecules fold into pseudoknot structures, which are often essential for the formation of an RNA’s 3D structure. Currently the design of RNA molecules, which fold into a specific structure (known as RNA inverse folding) within biotechnological applications, is lacking the feature of incorporating pseudoknot structures into the design. Hairpin-(H)- and kissing hairpin-(K)-type pseudoknots cover a wide range of biologically functional pseudoknots and can be represented on a secondary structure level.    Results  The RNA inverse folding program antaRNA, which takes secondary structure, target GC-content and sequence constraints as input, is extended to provide solutions for such H- and K-type pseudoknotted secondary structure constraint.  We demonstrate the easy and flexible interchangeability of modules within the antaRNA framework by incorporating pKiss as structure prediction tool capable of predicting the mentioned pseudoknot types. The performance of the approach is demonstrated on a subset of the Pseudobase ++ dataset.    Conclusions  This new service is available via a standalone version and is also part of the Freiburg RNA Tools webservice. Furthermore, antaRNA is available in Galaxy and is part of the RNA-workbench Docker image.

antaRNA – Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization