Table 1.
Feature descriptors calculated by iLearnPlus for protein sequences
| Descriptor group | Descriptor (abbreviation) | Reference |
|---|---|---|
| Amino acid composition | Amino acid composition (AAC) | (37) |
| Enhanced amino acid composition (EAAC) | (14,15) | |
| Composition of k-spaced amino acid pairs (CKSAAP) | (38,39) | |
| Kmer (dipeptides and tripeptides) composition (DPC and TPC) | (37,40) | |
| Dipeptide deviation from expected mean (DDE) | (40) | |
| Composition (CTDC) | (41–45) | |
| Transition (CTDT) | (41–45) | |
| Distribution (CTDD) | (41–45) | |
| Conjoint triad (CTriad) | (46) | |
| Conjoint k-spaced Triad (KSCTriad) | (14,15) | |
| Adaptive skip dipeptide composition (ASDC) | (47) | |
| PseAAC of distance-pairs and reduced alphabet (DistancePair) | (20,48) | |
| Grouped amino acid composition | Grouped amino acid composition (GAAC) | (14,15) |
| Grouped enhanced amino acid composition (GEAAC) | (14,15) | |
| Composition of k-spaced amino acid group pairs (CKSAAGP) | (14,15) | |
| Grouped dipeptide composition (GDPC) | (14,15) | |
| Grouped tripeptide composition (GTPC) | (14,15) | |
| Autocorrelation | Moran (Moran) | (49,50) |
| Geary (Geary) | (51) | |
| Normalized Moreau-Broto (NMBroto) | (52) | |
| Auto covariance (AC) | (53–55) | |
| Cross covariance (CC) | (53–55) | |
| Auto-cross covariance (ACC) | (53–55) | |
| Quasi-sequence-order | Sequence-order-coupling number (SOCNumber) | (56–58) |
| Quasi-sequence-order descriptors (QSOrder) | (56–58) | |
| Pseudo-amino acid composition | Pseudo-amino acid composition (PAAC) | (59,60) |
| Amphiphilic PAAC (APAAC) | (59,60) | |
| Pseudo K-tuple reduced amino acids composition (PseKRAAC_type 1 to type 16) | (61) | |
| Residue composition | Binary - 20bit (binary) | (62,63) |
| Binary - 6bit (binary_6bit) | (20,64) | |
| Binary - 5bit (binary_5bit_type 1 and type 2) | (20,65) | |
| Binary - 3bit (binary_3bit_type 1 to type 7) | (47) | |
| Learn from alignments (AESNN3) | (20,66) | |
| Overlapping property features - 10 bit (OPF_10bit) | (47) | |
| Overlapping property features - 7 bit (OPF_7bit type 1 to type 3) | (47) | |
| Physicochemical property | AAIndex (AAIndex) | (67) |
| BLOSUM matrix | BLOSUM62 (BLOSUM62) | (68) |
| Z-Scale index | Z-Scale (Zscale) | (69) |
| Similarity-based descriptor | K-nearest neighbor (KNN) | (70) |