CP design Server

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Find compatible sequences using inverse folding

Either upload a file containing a single RNA structure, paste in an RNA structure, or fill in fields in the verbose form.

File upload Paste input Verbose input

Fill the following fields:
Fasta comment

Target structure (required)


Use LNS Energy model:
Temperature (ÂșC): Dangling end treatment:

Base pair constraints
Structure of compatible base pairs

List of incompatible base pairs

Amino acid constraints
Target amino acid sequences
Expand search to similar amino acids based on
Search maximizing blosum similarity score

Or create your own compatibile aminoacid constraints using our dictionary

Starting positions of amino acid sequences

Energy constraints
Free energy: Min: Max:
Free energy minimization

Nucleotide composition
GC content: Min: Max:

Maximum consecutive nucleotides:
A: C: G: U:

Limit GC pairs:Min: Max:
Limit AU pairs:Min: Max:
Limit GU pairs:Min: Max:

Limit A bases: Min: Max:
Limit C bases: Min: Max:
Limit G bases: Min: Max:
Limit U bases: Min: Max: