Entropy

After generating LIPS results for protein 1xqf chain A, we can utilise them to annotate the protein at both the surface level and per-residue level.

In this tutorial, we demonstrate how to use TMKit to annotate each residue with entropy scores of the LIPS results that it belongs to.

Reminder of data

Please make sure that the build-in example dataset has been downloaded before you walk through the tutorial.

Example usage

We can first read the file of a helix surface ID id=1 using the following code. Please remember that we have put the results for protein 1xqf chain A in folder ./data/lips/ as in the last tutorial.

Code

import tmkit as tmk

df = tmk.feature.get_surf_entropy(
    fp='./data/lips/',
    prot_name='1xqf',
    file_chain='A',
    id=1,
)
print(df)

Output

     aa_ids   ents
0         2  1.158
1         5  6.798
2         6  4.896
3         9  4.852
4        12  3.694
..      ...    ...
150     352  4.846
151     355  4.551
152     356  3.724
153     359  3.276
154     362  4.539

[155 rows x 2 columns]

The output is a dataframe containing 2 columns, that is, aa_ids and ents, as shown below.

Attribute	Description
aa_ids	amino acid ID
ents	entropy score

If we want to annotate all amino acids with the entropy scores, we need to use all 7 surface data. In TMKit, we can do it this way.

Code

import tmkit as tmk

_, _, entropy_dict, _ = tmk.feature.read(
    fp='./data/lips/',
    prot_name='1xqf',
    file_chain='A',
)
print(entropy_dict)

Output

{1.0: 1.125, 4.0: 5.71, 5.0: 6.798, ..., 357.0: 5.976, 360.0: 1.749}

Actually, we can use TMKit to check the summary about all 7 surfaces, which shows the overall entropy score at the surface level.

Code

import tmkit as tmk

df = tmk.feature.get_helix_all_surf_entropy(
    fp='./data/lips/',
    prot_name='1xqf',
    file_chain='A',
)
print(df)

Output

   surfs   ents
0      5  4.846
1      0  4.912
2      3  4.852
3      1  4.885
4      2  4.749
5      6  4.746
6      4  4.948

Attributes

Attribute	Description
prot_name	name of a protein in the prefix of a PDB file name (e.g., 1xqf in 1xqfA.pdb)
file_chain	chain of a protein in the prefix of a PDB file name (e.g., A in 1xqfA.pdb)
fp	path where the LIPS results for a protein are placed
id	surface id, 0-6

See also

Please see here for better understanding the file-naming system.

Output

Please check the output in each vignette above.