MC-Tools

This program will generate an MC-Sym script that will build an RNA of the specified sequence and secondary structure. Please consider these points:

Accepted symbols for sequence are: `A`, `C`, `G`, `U` and `T`

Accepted symbols for structure are: `.`, `(`, `[`, `)` and `]`

Isolated base pairs .(. .). are not modeled if they are not within NCMs

Structures with more than 40% in single-stranded (i.e. non-structures) are not modeled

Classic secondary structures are difficult to model properly

Pseudoknots are accepted, as long as the expression is properly balanced

For advanced modeling topics please visit our FAQ

Name:

Sequence:

Structure:

Fragment RMSD: 0.1 0.5 1.0 1.5 2.0 3.0 Angstroms

Use Don't use high-resolution NCMs for canonical stacks of base pairs

Merge RMSD: 0.1 0.5 1.0 1.5 2.0 3.0 Angstroms

Clash threshold: 0.1 0.5 1.0 1.5 2.0 3.0 Angstroms

Bond threshold: 0.1 0.5 1.0 1.5 2.0 2.5 3.0 Angstroms

Construction method: Cyclic Coordinate Minimisation Interpolation Estimation

Exploration method: probabilistic exhaustive

Model limit: [min:1, max:9999]

Time limit: 5 minutes 10 minutes 15 minutes 30 minutes 1 hour 12 hours 1 day 2 days none

Model diversity: 0.1 0.5 1.0 1.5 2.0 3.0 5.0 Angstroms

Here, you can upload pdb files that you want to use as reference
Accepted file extensions are .pdb and .pdb.gz