Table 2 Description of each Characterizer contained in PCP-ML
From: PCP-ML: Protein characterization package for machine learning
Name of characterizer | Brief description of functionality provided |
|---|---|
AtchleyFactors | Characterizes five major aspects of an amino acid with real number values. The values were obtained via a statistical analysis of amino acids when looking at polarity, secondary structure, molecular size , amino acid composition and charge. These values were reported in [24]. |
InterfaceContactPotentials | Characterizes contact potential between two residues. These contact potentials come from a statistical analysis performed on contacts in protein interfaces. They were reported in [18]. |
BetaContactPotentials | Characterizes the contact potential for two residues in two beta sheets. These values come from a study of contact potentials of residues in cross strand pairings in beta sheets. They were reported in [22]. |
SSComposition | Determine the percentage of each secondary structure (SS) type in a string representing the secondary structure of the entire protein. |
SAComposition | Determine the percentage of solvent accessibility from a string representing the solvent accessibility of the entire protein. |
AAComposition | Determine the percentage of each amino acid in a protein sequence. |
Hydrophobicity | Characterizes the hydrophobicity of a residue. These values come from a study on hydrophobicity and helical propensity in [23]. |
CalculateR | Calculates the Pearson correlation coefficient for the elements of two feature vectors. |
CalculateCosine | Calculates the cosine between two feature vectors. |
ScaledOrderedMean | Calculates the nth ordered mean for the Amino Acid, Secondary Structure or Solvent Accessibility string. |
CalculateEntropy | Calculates the Shannon entropy for a vector of probabilities |