SimRNA

Load one of the examples:

Tetraloop (quick testing case example - execution time ~1-2 min):

Viral RNA Psedoknot:

Two chain RNA with hard secondary structure restraints:

Example for hard pairing restraints with sequence:

Example for predicting alternative structure using soft restraints

Example for usage of chemical probing data as restriaints

Example for folding a G-quadruplex using hard pairing restraints

Model your RNA

Job Title^*: ?

A job name is mandatory for submitting a job.

E-mail: (optional) ?

By providing your email, we can inform you about the status of your submitted job.

Inputs for Simulation

Basic Inputs

Input^*: ?

Specify the input structure type and provide the corresponding input structure in the appropriate format.
For the sequence, provide a single-line input containing "A, C, G, and U" with each chain separated by a space.
For more details click or check "3. Format of structure input files"

PDB/mmCIF restraints ?

If the input is in PDB/mmCIF format, selecting this option will restrict the movement of atoms based on B-factor and occupancy.
for more details click

Hard seconary structure restraints: ?

With this type of secondary structure restraints, SimRNA is compelled to generate the requested secondary structure.
for more details click

Advanced Inputs

Advanced Options

What do you want to model?^*

If you are not a robot, write RNA.

SimRNAweb2.0

Load one of the examples:

Model your RNA

Inputs for Simulation

Basic Inputs

Advanced Inputs

Advanced Options

Simulation configurations

Clustering options

SimRNAweb2.0

Load one of the examples:

Model your RNA

Inputs for Simulation

Basic Inputs

Advanced Inputs Show

Advanced Options Show

Simulation configurations

Clustering options

Advanced Inputs

Advanced Options