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.
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  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.