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If you want to model an RNA sequence, search for potential templates in PDB (a database of experimental structures) and/or RFAM (a database of RNA familes). [External]
To preform RNA secondary structure prediction, we recommend to use (one of many servers) RNAfold. [External]
The group of tools aims to facilitate analysis of RNA 3D structure.
Get sequences get sequences of a bunch of PDB files
Standardize PDB files (get-rnapuzzle-ready, "_rpr.pdb") get a standardized naming of atoms, residues, chains to be compatible with the format proposed by the RNA-Puzzles community [report and add missing atoms], removes water and ions, keeps only canonical RNA atoms
The group of tools aims to facilitate operations on RNA 3D structure.
Concatenate merge a bunch of PDB files into one fileDe novo modeling (not based on fragments taken from the PDB database, usually better for modeling new folds, modeling structures without homologs with known structures)
Fragment-based modeling (fragments taken from the PDB database, usually better for modeling with close homologs with known structures)