COMPUTE PROTEIN

Amino acid properties:

We have considered physical, chemical, energetic and conformational properties and list of properties from AAindex database.

The change in property value upon mutation is calculated using following formula:

Δ P_mutation = P_Snp - P_wild-type             (1)
Where P_wild-type and P_Snp are the property values of wild-type and mutant residues, respectively and ΔP_mutation is the change in property due to mutation

Average property value is calculated using the formula:

$$\text"<Property>"_\text"protein"={∑↙{i=0}↖n property_i}/N \text'            (2)'$$

Where propety_i is the value of amino acid for each property and N is the length of Protein sequence.

Substitution matrices:

Amino acid mutation matrices are collected from AAIndex2 database and the mutation value is directly obtained from the matrices. Properties are calculated using the difference between the value of wild-type and mutant residue using equation (1).

Pairwise properties and contact potentials:

Pair-wise contact potentials matrices are collected from AAIndex3 database and difference of amino acid contact potential for a mutation is obtained by subtracting contact potential value of N-/C-neighbour of mutation position to wild type residue from N-/C-neighbour to mutant residue.