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]
RNA secondary structure tools
To preform RNA secondary structure prediction, we recommend to use (one of many servers) RNAfold. [External]
RNA 3D structure conversion from CIF to PDB
Convert CIF files to PDB
Convert PDB files to CIF
RNA 3D structure analysis
The group of tools aims to facilitate analysis of RNA 3D structure.
get sequences of a bunch of PDB files
Get secondary structures
get secondary structures of a bunch of PDB files
Analysis with X3DNA
get statistics and details on PDB files
Analysis with ClaRNA
get interactions detected for PDB files
RNA 3D structure standardization
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
Standardize PDB files for Molecular Dynamics (get-molecular-dynamics-ready, "_mdr.pdb")
get a standardized naming of atoms, residues, chains to be compatible with the format used e.g., by openmm [report and add missing atoms], removes water and ions, keeps only canonical RNA atoms
RNA 3D structure editing
The group of tools aims to facilitate operations on RNA 3D structure.
merge a bunch of PDB files into one file
extract parts of PDB files
delete parts of PDB files
HETATM with ATOM in PDB files
edit (not the same as mutate) of PDB files
mutate residues in PDB files
swap names of the chains in PDB files
replace XYZ coordinates of one PDB file with XYZ coordinates from another file
RNA 3D structure minimization
Remove steric clashes, optimize bonds angles.
Should be used to to molecules in reach of RNA 3D structure prediction, so of length of 150 bp.
Minimize with QRNAS
minimize PDB files to fix clashes based on QRNAS [this can take up to 1h]
Minimize with OpenMM
minimize PDB files to fix clashes based on OpenMM [this can take up to 1h]
RNA 3D structures comparison
it is a simple tool to compare two files of PDB format to identify the difference in the annotation of atoms, missing atoms, missing fragments
Calculate Root Mean Square Deviation (RMSD)
RMSD is the measure of the average distance between the atoms of superimposed RNAs (also proteins etc.). This is a simple, geometrical measure.
Calculate Network Interaction Fidelity (INF)
INF is the measure specific for RNA molecules. RNAs are represented by network of interactions, and the closes two networks of interactions of two molecules are similar, the higher INF.
RNA 3D model quality assessment
tools to assess how good are the models obtained from modeling procedure.
RNA 3D modeling [External servers]
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)
Rosetta Stepwise Monte Carlo Protocol
Fragment-based modeling (fragments taken from the PDB database, usually better for modeling with close homologs with known structures)
The RNAComposer system offers a new user-friendly approach to the fully automated prediction of large RNA 3D structures. The method is based on the machine translation principle and operates on the RNA FRABASE database acting as the dictionary relating RNA secondary structure and tertiary structure elements.
Send us feedback what kind of tools do you need in your modeling pipeline.
We are exploring using https://piwik.pro to track usage of the server for grant proposals, scientific presentations.
Please write to us if there is any problem with your job mail us [behind Apple Hide My Mail].
You can also write an empty mail to sign to our Google Group to ask questions and shape the tools! Join our Google Group or write an empty e-mail to email@example.com.