Skip to main content
. 2014 May 18;2014:715494. doi: 10.1155/2014/715494

Table 2.

Summary of the considered features, where y denotes one of the three secondary structure states and x denotes one of the 20 common AAs.

Feature sets Description
Sequence-based (79) Sequence length (1)
Composition vector (20)
The number of AAs in the sequence belonging to {R group, Electronic group, Hydrophobicity group, Exchange group} (18)
First and second order composition moment vector (40)

PSSM-based (203) From the PSSM matrix

Secondary structure (217) Based on the features utilized in the PSI-Pred method (90)
Based on the predicted secondary structure which describes collocation
of helical and strand segments (127)

Average RSA based (23) Average RSA of the residues with AA type x (20)
Average RSA of the residues with secondary structure type y (3)

Average isoelectric point (1) pI = 1/Ni=1 N pI i, the pI i values in the paper [11]

Auto-correlation functions based on FHi, EHi, and Hp indices (25) A n a = 1/(Nn)∑i=1 Nn a i a i+n, where a defines the corresponding physicochemical properties, such as two hydrophobicity indices (the Fauchere-Pliska's (FH) with n = 1,2,…, 10 and the Eisenberg's (EH) n = 1,2,…, 6), and hydropathy (HP) index with n = 1,2,…, 9.

Auto-correlation functions based on cumulative FHi index (6) A n a = ∑i=1 Nn(∑j=1 i a j) × (∑j=1 i+n a j)/(Nn), where a is the FH index with n = 1,2,…, 6.

Sum of hydrophobicities based on FHi and EHi (2) H sum a = ∑i=1 N a i, where a is the FH or the EH index.

R groups (5) RGi, where i = 1 corresponds to nonpolar aliphatic AAs (AVLIMG), i = 2 to polar uncharged AAs (SPTCNQ), i = 3 to positively charged AAs (KHR), i = 4 to negative AAs (DE), and i = 5 to aromatic AAs (FYW); the composition percentage of each group in the sequence is computed

Electronic groups (5) EGi, where i = 1corresponds to electron donor AAs (DEPA), i = 2 to weak electron donor AAs (LIV), i = 3 to electron acceptor AAs (KNR), i = 4 to weak electron acceptor AAs (FYMTQ), and i = 5 to neutral AAs (GHWS); the composition percentage of each group in the sequence is computed

Blast based (30) Refer to subsection “Features

GLAM2-based (30) Refer to subsection “Features

GIBBS-based (6) Refer to subsection “Features
HHS Vulnerability Disclosure