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If you want to model an RNA sequence, search for potential templates in PDB and/or RFAM.
Web wrappers to this tools are in progress. You can find more on wrappers that you can run in your terminal here.The second group of tools aims to facilitate operations on RNA secondary structure.
Secondary structure prediction RNA secondary structure prediction are implemented, including RNAsubopt, RNAeval, RNAfold from ViennaRNA, CentroidFold, ContextFold, MC-Fold and IPknot. rna-tools -> online - in progress
The group of tools aims to facilitate analysis of RNA 3D structure.
Analysis with X3DNA get statistics and details on PDB filesThe group of tools aims to facilitate operations on RNA 3D structure.
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
De 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)