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RAG Builder

RAG Builder produces atomic models for a target RNA 2D structure and corresponding 3D tree graph [3]. The target 3D tree graphs are generated by graph sampling (see RAG Sampler).

Please provide the RNA 2D structure file (.bpseq format) and target 3D tree graph file (.pdb format). We suggest uploading the lowest scoring graph produced by RAG Sampler. This server currently does not accept RNA structures with over 200 nucleotides.

For file format details, see Information page or download a sample 2D structure and corresponding 3D graph file. To run RAG Builder with the sample input, submit with both file fields blank.

Show Algorithm Description ▼

RAG Builder uses our F-RAG (fragment assmebly for RNA-As-Graphs) algorithm to build atomic models. First, RAG-3D partitioning and search [13] is run to divide the target graph into subgraphs [13, 14] and return the best matching atomic fragments for each subgraph, that are then used as input for F-RAG. F-RAG assembles the atomic fragments using nucleotides corresponding to common graph vertices. All models are scored using the knowledge-based potential created for 3D tree graph topology sampling [1, 2]. The generated models are then filtered based on number of nucleotides and their score.

See the full description of our fragment assembly protocol: F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly.

Secondary Structure File:

Target 3D Tree Graph:

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