gt4sd.properties.proteins.functions module¶

Summary¶

Functions:

`aliphatic_index`	Computes the aliphatic index of a protein.
`aromaticity`	Computes aromaticity of the protein (relative frequency of Phe+Trp+Tyr).
`boman_index`	Computes the Boman index of a protein (sum of solubility values of all residues).
`charge`	Computes the charge of a protein.
`charge_density`	Computes the charge density of a protein.
`hydrophobic_ratio`	Computes the hydrophobicity of a protein, relative freq.
`instability`	Calculates the protein instability.
`isoelectric_point`	Computes the isoelectric point of every residue and aggregates.
`length`	Retrieves the number of residues of a protein.
`molecular_weight`	Computes the molecular weight of a protein.

Reference¶

length(protein)[source]¶

Retrieves the number of residues of a protein.

Return type: int

molecular_weight(protein, amide=False)[source]¶

Computes the molecular weight of a protein.

Return type: float

boman_index(protein)[source]¶

Computes the Boman index of a protein (sum of solubility values of all residues).

Boman, H. G. (2003). Antibacterial peptides: basic facts and emerging concepts. Journal of internal medicine, 254(3), 197-215.

Return type: float

aliphatic_index(protein)[source]¶

Computes the aliphatic index of a protein. Measure of thermal stability.

Ikai, A. (1980). Thermostability and aliphatic index of globular proteins. The Journal of Biochemistry, 88(6), 1895-1898.

Return type: float

hydrophobic_ratio(protein)[source]¶

Computes the hydrophobicity of a protein, relative freq. of A,C,F,I,L,M & V.

Return type: float

charge(protein, ph=7.0, amide=False)[source]¶

Computes the charge of a protein.

Bjellqvist, B., Hughes, G. J., Pasquali, C., Paquet, N., Ravier, F., Sanchez, J. C., … & Hochstrasser, D. (1993). The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis, 14(1), 1023-1031.

Return type: float

charge_density(protein, ph=7.0, amide=False)[source]¶

Computes the charge density of a protein.

Bjellqvist, B., Hughes, G. J., Pasquali, C., Paquet, N., Ravier, F., Sanchez, J. C., … & Hochstrasser, D. (1993). The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis, 14(1), 1023-1031.

Return type: float

isoelectric_point(protein, amide=False)[source]¶

Computes the isoelectric point of every residue and aggregates.

Return type: float

aromaticity(protein)[source]¶

Computes aromaticity of the protein (relative frequency of Phe+Trp+Tyr).

Lobry, J. R., & Gautier, C. (1994). Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage

in 999 Escherichia coli chromosome-encoded genes.

Nucleic acids research, 22(15), 3174-3180.

Return type: float

instability(protein)[source]¶

Calculates the protein instability.

Guruprasad, K., Reddy, B. B., & Pandit, M. W. (1990). Correlation between stability of a protein and its dipeptide composition: a novel

approach for predicting in vivo stability of a protein from its primary sequence.

Protein Engineering, Design and Selection, 4(2), 155-161.

Return type: float