Incorporating ligands binding to specific sequence/structure motifs using soft constraints

Overview

Ligand binding to specific hairpin/interior loop like motifs using the Soft constraints feature. More…

// global functions

int vrna_sc_add_hi_motif (
    vrna_fold_compound_t* vc,
    const char* seq,
    const char* structure,
    FLT_OR_DBL energy,
    unsigned int options
    )

Detailed Documentation

Ligand binding to specific hairpin/interior loop like motifs using the Soft constraints feature.

Here is an example that adds a theophylline binding motif. Free energy contribution is derived from :math:`k_d = 0.32 mu mol / l ` , taken from Jenison et al. 1994

_images/theo_aptamer.svgtheo_aptamer
vrna_sc_add_hi_motif(vc,
                   "GAUACCAG&CCCUUGGCAGC",
                   "(...((((&)...)))...)",
                   -9.22, VRNA_OPTION_DEFAULT);

Global Functions

int vrna_sc_add_hi_motif (
    vrna_fold_compound_t* vc,
    const char* seq,
    const char* structure,
    FLT_OR_DBL energy,
    unsigned int options
    )
Add soft constraints for hairpin or interior loop binding motif.

SWIG Wrapper Notes This function is attached as method sc_add_hi_motif() to objects of type fold_compound

Parameters:

vc The vrna_fold_compound_t the motif is applied to
seq The sequence motif (may be interspaced by ‘&’ character
structure The structure motif (may be interspaced by ‘&’ character
energy The free energy of the motif (e.g. binding free energy)
options Options

Returns:

non-zero value if application of the motif using soft constraints was successful