Tools

Sequence search

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 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, keeps/adds OP3 atom at the beginning of a chain

RNA 3D structure editing

The group of tools aims to facilitate operations on RNA 3D structure.

Concatenate merge a bunch of PDB files into one file
Extract extract parts of PDB files
Delete delete parts of PDB files
Replace HETATM with ATOM in PDB files
Edit edit (not the same as mutate) of PDB files
Mutate mutate residues in PDB files
Swap chains swap names of the chains in PDB files
Replace replace XYZ coordinates of one PDB file with XYZ coordinates from another file

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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

diffpdb 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

Assess 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)

RNAComposer

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.

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Send us feedback what kind of tools do you need in your modeling pipeline.

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