Description Usage Arguments Details Value Author(s) See Also Examples
This function allows to get values of entropy/conservation for amino acids dispersed in sequence of given protein. It works well with a list of dispersed amino acids in one protein.
1 | get_structures_entropy(structure_index,score_list)
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structure_index |
A is a list of indices in alignment of protein and structures. Output output of |
score_list |
A list of entropies for whole alignment |
This function allows to obtain entropy (calculated on MSA) for dispersed amino acids in protein e.g. surface, binding site, tunnels etc. The input is a list of few structure indices in given protein sequence. Function calculates position of those in aligned sequence and returns a vector/matrix or a list of matrices with entropy values.
structure_entropies |
A list of matrices. Rows are entropy scores, columns are |
Alicja Pluciennik & Michal Stolarczyk
create_structure_seq
, read_structure
1 2 3 4 5 6 7 8 9 10 11 12 | data("structure")
data("alignment")
#creating library uniprot - PDB
uniprot="P34914"
tunnel=create_structure_seq(structure,uniprot,alignment)
indices=get_structures_idx(structure)
protein_index = indices$proteinIndices
structure_index = indices$structureIndices
entropy_scores_list=list(Schneider_entropy = schneider_conservativity(alignment),
Escore_entropy = Escore_conservativity(alignment))
structure_entropy=get_structures_entropy(structure_index, entropy_scores_list)
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