Table 2
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Different types of features employed by the reviewed approaches for AMP prediction

Feature typeFeatureReference
Composition featuresAAC[20, 28, 64, 82, 83, 98, 103, 104, 112, 113]
 Normalized amino acid composition (NAAC)[20]
 AAPC[105]
 DPC[3, 18, 64, 71, 112, 122]
 TPC[3, 18, 64]
 Peptide length[49, 89]
 N-gram composition found by counting (NCC)[103]
 N-gram composition found by t-test (NTC)[103]
 Motifs composition (MC)[103]
Position featuresN-gram binary profiling of position found by counting (NCB)[103]
 N-gram binary profiling of position found by t-test (NTB)[103]
 Motifs binary profiling of position (MB)[103]
 PSSM profile[108]
 CMV[71]
Structure featuresα-Helix[20, 49–51, 64, 65, 85, 89, 98]
 β-Sheet[20, 49–51, 64, 65, 85, 89, 98]
 β-Turn[20, 49–51, 64, 85, 89, 98]
 Loop formation[65]
 Random coil[51, 85]
Physicochemical propertiesIsoelectric point[20, 49, 81, 85]
 Charge[3, 18, 20, 51, 65, 81, 98]
 Molecular mass[50]
 Atom count[50]
 Size[81]
 Amino acid acidity and basicity[81]
 Aromaticity[81]
 Sulfur[81]
 Oxygen, nitrogen, hydrogen and carbon atom contents[81]
 Net charge at the physiological pH[63]
 μH[63]
 Aliphatic index[3, 18, 81]
 Amphipathicity[51, 65]
 Ratio between hydrophobic and charged residues[63]
 Hydrophilicity[3, 18]
 Hydrophobic moment[63, 65]
 Hydrophobicity[3, 18, 20, 51, 63, 65, 89, 98]
 Instability index[3, 18]
 Disordering[51]
 Solvent accessibility[98]
 Surface tension[98]
 Normalized van der Waals volume[64, 98]
 Conformational similarity[64]
 Polarity[64, 81, 98]
 Polarizability[64, 98]
 Flexibility[65]
 Normalized MoreauBroto autocorrelation (NMBroto)[71]
 Moran autocorrelation (Moran)[71]
 Geary autocorrelation (Geary)[71]
 CNMR[81]
 Composition/transition/distribution (CTD)[3, 18, 64, 71, 92, 95, 98, 103, 104]
 PseAAC[19, 20, 66, 71, 80, 83, 96, 98, 103, 113]
 PseKRAAC[113]
 3-mer composition[82]
 Sequence order coupling number[71]
 Quasi sequence order[71]
Similarity featuresBLOSUM-50[3, 18, 64]
 LZ complexity pairwise similarity scores[74]
In vivo propensityIn vivo aggregation propensity[85, 89]
 In vivo stability[64]
Feature typeFeatureReference
Composition featuresAAC[20, 28, 64, 82, 83, 98, 103, 104, 112, 113]
 Normalized amino acid composition (NAAC)[20]
 AAPC[105]
 DPC[3, 18, 64, 71, 112, 122]
 TPC[3, 18, 64]
 Peptide length[49, 89]
 N-gram composition found by counting (NCC)[103]
 N-gram composition found by t-test (NTC)[103]
 Motifs composition (MC)[103]
Position featuresN-gram binary profiling of position found by counting (NCB)[103]
 N-gram binary profiling of position found by t-test (NTB)[103]
 Motifs binary profiling of position (MB)[103]
 PSSM profile[108]
 CMV[71]
Structure featuresα-Helix[20, 49–51, 64, 65, 85, 89, 98]
 β-Sheet[20, 49–51, 64, 65, 85, 89, 98]
 β-Turn[20, 49–51, 64, 85, 89, 98]
 Loop formation[65]
 Random coil[51, 85]
Physicochemical propertiesIsoelectric point[20, 49, 81, 85]
 Charge[3, 18, 20, 51, 65, 81, 98]
 Molecular mass[50]
 Atom count[50]
 Size[81]
 Amino acid acidity and basicity[81]
 Aromaticity[81]
 Sulfur[81]
 Oxygen, nitrogen, hydrogen and carbon atom contents[81]
 Net charge at the physiological pH[63]
 μH[63]
 Aliphatic index[3, 18, 81]
 Amphipathicity[51, 65]
 Ratio between hydrophobic and charged residues[63]
 Hydrophilicity[3, 18]
 Hydrophobic moment[63, 65]
 Hydrophobicity[3, 18, 20, 51, 63, 65, 89, 98]
 Instability index[3, 18]
 Disordering[51]
 Solvent accessibility[98]
 Surface tension[98]
 Normalized van der Waals volume[64, 98]
 Conformational similarity[64]
 Polarity[64, 81, 98]
 Polarizability[64, 98]
 Flexibility[65]
 Normalized MoreauBroto autocorrelation (NMBroto)[71]
 Moran autocorrelation (Moran)[71]
 Geary autocorrelation (Geary)[71]
 CNMR[81]
 Composition/transition/distribution (CTD)[3, 18, 64, 71, 92, 95, 98, 103, 104]
 PseAAC[19, 20, 66, 71, 80, 83, 96, 98, 103, 113]
 PseKRAAC[113]
 3-mer composition[82]
 Sequence order coupling number[71]
 Quasi sequence order[71]
Similarity featuresBLOSUM-50[3, 18, 64]
 LZ complexity pairwise similarity scores[74]
In vivo propensityIn vivo aggregation propensity[85, 89]
 In vivo stability[64]
Table 2
Open in new tab

Different types of features employed by the reviewed approaches for AMP prediction

Feature typeFeatureReference
Composition featuresAAC[20, 28, 64, 82, 83, 98, 103, 104, 112, 113]
 Normalized amino acid composition (NAAC)[20]
 AAPC[105]
 DPC[3, 18, 64, 71, 112, 122]
 TPC[3, 18, 64]
 Peptide length[49, 89]
 N-gram composition found by counting (NCC)[103]
 N-gram composition found by t-test (NTC)[103]
 Motifs composition (MC)[103]
Position featuresN-gram binary profiling of position found by counting (NCB)[103]
 N-gram binary profiling of position found by t-test (NTB)[103]
 Motifs binary profiling of position (MB)[103]
 PSSM profile[108]
 CMV[71]
Structure featuresα-Helix[20, 49–51, 64, 65, 85, 89, 98]
 β-Sheet[20, 49–51, 64, 65, 85, 89, 98]
 β-Turn[20, 49–51, 64, 85, 89, 98]
 Loop formation[65]
 Random coil[51, 85]
Physicochemical propertiesIsoelectric point[20, 49, 81, 85]
 Charge[3, 18, 20, 51, 65, 81, 98]
 Molecular mass[50]
 Atom count[50]
 Size[81]
 Amino acid acidity and basicity[81]
 Aromaticity[81]
 Sulfur[81]
 Oxygen, nitrogen, hydrogen and carbon atom contents[81]
 Net charge at the physiological pH[63]
 μH[63]
 Aliphatic index[3, 18, 81]
 Amphipathicity[51, 65]
 Ratio between hydrophobic and charged residues[63]
 Hydrophilicity[3, 18]
 Hydrophobic moment[63, 65]
 Hydrophobicity[3, 18, 20, 51, 63, 65, 89, 98]
 Instability index[3, 18]
 Disordering[51]
 Solvent accessibility[98]
 Surface tension[98]
 Normalized van der Waals volume[64, 98]
 Conformational similarity[64]
 Polarity[64, 81, 98]
 Polarizability[64, 98]
 Flexibility[65]
 Normalized MoreauBroto autocorrelation (NMBroto)[71]
 Moran autocorrelation (Moran)[71]
 Geary autocorrelation (Geary)[71]
 CNMR[81]
 Composition/transition/distribution (CTD)[3, 18, 64, 71, 92, 95, 98, 103, 104]
 PseAAC[19, 20, 66, 71, 80, 83, 96, 98, 103, 113]
 PseKRAAC[113]
 3-mer composition[82]
 Sequence order coupling number[71]
 Quasi sequence order[71]
Similarity featuresBLOSUM-50[3, 18, 64]
 LZ complexity pairwise similarity scores[74]
In vivo propensityIn vivo aggregation propensity[85, 89]
 In vivo stability[64]
Feature typeFeatureReference
Composition featuresAAC[20, 28, 64, 82, 83, 98, 103, 104, 112, 113]
 Normalized amino acid composition (NAAC)[20]
 AAPC[105]
 DPC[3, 18, 64, 71, 112, 122]
 TPC[3, 18, 64]
 Peptide length[49, 89]
 N-gram composition found by counting (NCC)[103]
 N-gram composition found by t-test (NTC)[103]
 Motifs composition (MC)[103]
Position featuresN-gram binary profiling of position found by counting (NCB)[103]
 N-gram binary profiling of position found by t-test (NTB)[103]
 Motifs binary profiling of position (MB)[103]
 PSSM profile[108]
 CMV[71]
Structure featuresα-Helix[20, 49–51, 64, 65, 85, 89, 98]
 β-Sheet[20, 49–51, 64, 65, 85, 89, 98]
 β-Turn[20, 49–51, 64, 85, 89, 98]
 Loop formation[65]
 Random coil[51, 85]
Physicochemical propertiesIsoelectric point[20, 49, 81, 85]
 Charge[3, 18, 20, 51, 65, 81, 98]
 Molecular mass[50]
 Atom count[50]
 Size[81]
 Amino acid acidity and basicity[81]
 Aromaticity[81]
 Sulfur[81]
 Oxygen, nitrogen, hydrogen and carbon atom contents[81]
 Net charge at the physiological pH[63]
 μH[63]
 Aliphatic index[3, 18, 81]
 Amphipathicity[51, 65]
 Ratio between hydrophobic and charged residues[63]
 Hydrophilicity[3, 18]
 Hydrophobic moment[63, 65]
 Hydrophobicity[3, 18, 20, 51, 63, 65, 89, 98]
 Instability index[3, 18]
 Disordering[51]
 Solvent accessibility[98]
 Surface tension[98]
 Normalized van der Waals volume[64, 98]
 Conformational similarity[64]
 Polarity[64, 81, 98]
 Polarizability[64, 98]
 Flexibility[65]
 Normalized MoreauBroto autocorrelation (NMBroto)[71]
 Moran autocorrelation (Moran)[71]
 Geary autocorrelation (Geary)[71]
 CNMR[81]
 Composition/transition/distribution (CTD)[3, 18, 64, 71, 92, 95, 98, 103, 104]
 PseAAC[19, 20, 66, 71, 80, 83, 96, 98, 103, 113]
 PseKRAAC[113]
 3-mer composition[82]
 Sequence order coupling number[71]
 Quasi sequence order[71]
Similarity featuresBLOSUM-50[3, 18, 64]
 LZ complexity pairwise similarity scores[74]
In vivo propensityIn vivo aggregation propensity[85, 89]
 In vivo stability[64]
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