SimRNA

Load one of the examples:

Model your RNA

Please run max. 2 jobs at the same time. If you need to run more jobs, please consider installing SimRNA locally at your own computer. Sorry for any inconvenience!

In the queue there are 3 jobs and 6 currently running at the cluster.
To process your job it might take up to 3 days, 3 hours.
(2 jobs at the same time, avg. job 6-10h, if the cluster is free)

E-mail address is optional

Please, remember an RNA sequence OR an RNA structure is required to do prediction.

RNA sequence (length limit 200nt!)
This server predicts RNA 3D structure, so please use only continuous strings of G,C,A,U to indicate RNA sequence (no Ts! please replace them by Us). The space character is used to indicate chain breaks.

RNA secondary structure (in dot-bracket notation) [optional]

RNA structure (in the PDB format) to use in the simulation (as a starting point) [optional]:

Select file Change Remove

e.g. A:1-10,15,25-30 ; B:1-10 residues to freeze (they do not move in the simulation). Keep empty to allow moving all residues.

Restraints (in the SimRNA restraints format, text file, read more) [optional]

Select file Change Remove

restraints file loaded unmodified_tRNAPhe_restraints.txt

Advanced parameters

Number of steps simulation: default = 500; max = 1000; min = 10, use only for a short RNA and testing
% of the lowest energy frames taken to clustering: e.g. 1 (default value) indicates that 1% of the lowest energy frames of an input trafl will be subjected for clustering (where the remaining frames will be ignored)

What do you want to model?

SimRNAweb

Load one of the examples:

Model your RNA

Advanced parameters