Incorporating Ligands Binding to Specific Sequence/Structure Motifs using Soft Constraints

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

Detailed Description

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 , taken from Jenison et al. 1994

vrna_sc_add_hi_motif(vc,
                   "GAUACCAG&CCCUUGGCAGC",
                   "(...((((&)...)))...)",
                   -9.22, VRNA_OPTION_DEFAULT); 

Collaboration diagram for Incorporating Ligands Binding to Specific Sequence/Structure Motifs using Soft Constraints:

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...

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/constraints/ligand.h>

Add soft constraints for hairpin or interior loop binding motif.

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

SWIG Wrapper Notes:

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