RAG Designer designs sequences and corresponding atomic models that fold onto a target RNA-like tree graph topology .
Please provide the target tree graph topology file in the form of an adjacency matrix. This server currently does not accept RNA target topologies with over 13 vertices.
For file format details, see the Information page or download a sample adjacency matrix file. To run RAG Designer with the sample input, submit with the file field blank.
If you would like to create an adjacency matrix corresponding to a specific 2D structure, please use the RNA Matrix Program.
Show Pipeline Description ▼
RAG Builder uses our F-RAG (fragment assembly for RNA-As-Graphs) to design sequences. The target tree graph topology is divided into subgraphs using graph partitioning , and corresponding atomic fragments for each subgraph are extracted from the RAG-3D database (used as input for F-RAG). F-RAG then assembles the atomic fragments for each subgraph using common loops and vertices to generate a full 3D atomic model. All models are scored using our knowledge-based statistical potential created for RAGTOP's 3D structure prediction [1, 2]. Unique sequences corresponding to lowest scoring models are then screened using two structure prediction programs, RNAfold  and NUPACK [16, 17, 18], and only sequences that are predicted to fold onto the target topology by both programs are reported.
See the full description of our design pipeline: A pipeline for computational design of novel RNA-like topologies.