Ligands Binding to RNA Structures

Basic Ligand Binding API

Simple Extensions to Model Ligand Binding to RNA Structures.

Unstructured Domains

Add ligand binding to loop regions using the Unstructured Domains feature.

Hairpin-/Internal Loop Motifs

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

Typedefs

typedef struct vrna_sc_motif_s vrna_sc_motif_t

Type definition for soft constraint motif.

#include <ViennaRNA/constraints/ligand.h>

Functions

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

Add soft constraints for hairpin or internal loop binding motif.

#include <ViennaRNA/constraints/ligand.h>

Here is an example that adds a theophylline binding motif. Free energy contribution is derived from \(k_d = 0.1 \mu M\), taken from Jenison et al. 1994. At \(1M\) concentration the corresponding binding free energy amounts to \(-9.93~kcal/mol\).

vrna_sc_add_hi_motif(fc,
"GAUACCAG&CCCUUGGCAGC",
"(...((((&)...)))...)",
                     -9.93, VRNA_OPTION_DEFAULT);

SWIG Wrapper Notes:

This function is attached as method sc_add_hi_motif() to objects of type fold_compound. The last parameter is optional an defaults to options = VRNA_OPTION_DEFAULT. See, e.g. RNA.fold_compound.sc_add_hi_motif() in the The RNA Python module .

Parameters:

• fc – 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

vrna_sc_motif_t *vrna_sc_ligand_detect_motifs(vrna_fold_compound_t *fc, const char *structure)

#include <ViennaRNA/constraints/ligand.h>

vrna_sc_motif_t *vrna_sc_ligand_get_all_motifs(vrna_fold_compound_t *fc)

#include <ViennaRNA/constraints/ligand.h>

struct vrna_sc_motif_s

Public Members

int i

#include <ViennaRNA/constraints/ligand.h>

int j

#include <ViennaRNA/constraints/ligand.h>

int k

#include <ViennaRNA/constraints/ligand.h>

int l

#include <ViennaRNA/constraints/ligand.h>

int number

#include <ViennaRNA/constraints/ligand.h>