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Masonry
RNAMasonry
Load the examples:
tRNA testing case example with SAXS data - execution time ~3-5 min
Model your RNA
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RNA
Please, remember an
RNA sequence (limit of length 150 nt) with secondary structure OR
RNA structure
(in the PDB/mmCIF format) is required to do prediction.
Sequence length
0
of of allowed 150 nt.
RNA secondary structure (in dot-bracket notation)
The secondary structure input can consist of several lines for encoding pseudo-knots.
RNA structure (in the PDB/mmCIF format) to use in the simulation (as a starting point)
Select file
Change
Remove
The input file should contain RNA only. Modelling of RNA-protein complexes is not supported yet.
SAXS [optional]
Restrain folding with a SAXS curve. Please remember to
acknowledge
the use of CRYSOL or FoXS
FOXS
CRYSOL
Select file
Change
Remove
Text file with a SAXS curve. Make sure it is accepted by CRYSOL and FoXS.
restraints file loaded
tRNA_saxs.dat
Residues to freeze [optional]
Residues to freeze:
e.g. 12:25,30:39, residues to freeze (they do not move in the simulation). Keep empty to allow moving all residues.
Number of steps of simulation [optional]
Number of steps of simulation:
What do you want to model?
Predict!