RNAlib-2.2.7
Incorporating ligands binding to specific sequence/structure motifs

This module covers functions that enable the incorporation of ligand binding free energies to specific hairpin/interior loop motifs by means of generic soft constraints. More...

+ Collaboration diagram for Incorporating ligands binding to specific sequence/structure motifs:

Files

file  ligand.h
 Functions for incorporation of ligands binding to haipirn and interior loop motifs.
 

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. More...
 

Detailed Description

This module covers functions that enable the incorporation of ligand binding free energies to specific hairpin/interior loop motifs by means of generic soft constraints.

Function Documentation

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

#include <ViennaRNA/ligand.h>

Add soft constraints for hairpin or interior loop binding motif.

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

"GAUACCAG&CCCUUGGCAGC",
"(...((((&)...)))...)",
-9.22, VRNA_OPTION_DEFAULT);
Parameters
vcThe vrna_fold_compound_t the motif is applied to
seqThe sequence motif (may be interspaced by '&' character
structureThe structure motif (may be interspaced by '&' character
energyThe free energy of the motif (e.g. binding free energy)
optionsOptions
Returns
non-zero value if application of the motif using soft constraints was successful