NanoTiler is a Java application for the design of RNA nanostructures. Among other things, it can accomplish the following: 1) Detection, extraction and annotation of RNA structural elements, 2) Use of RNA building blocks for assemblying larger structures, 3) Combinatorial search of building blocks 4) Optimization of building block positions 5) Topology classification 6) Sequence Optimization (i.e. sequence design for self-assembly into the given topology).
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Methods. 2011 Jun;54(2):239-50. Epub 2010 Dec 14.
Use of RNA structure flexibility data in nanostructure modeling.
Kasprzak W, Bindewald E, Kim TJ, Jaeger L, Shapiro BA.