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. 2018 Jul 31;20(5):1878–1912. doi: 10.1093/bib/bby061

Table 3.

Categories of target descriptors based on the properties they describe

Descriptor category Descriptor type Citations
Sequence composition

  • Amino acid composition (AAC)

  • Dipeptide composition (DC)

  • Tripeptide composition (TC)

 [82–85]
Physico-chemical properties

  • Autocorrelation (normalized Moreau-Broto, Moran and Geary)

  • Composition, transition and distribution (CTD)

  • Conjoint triad (CTriad)

  • Sequence-order-coupling number (SOCN)

  • Quasi-sequence-order descriptors (QSO)

  • Pseudo amino acid composition (Pse-AAC)

  • Amphiphilic pseudo amino acid composition (Am-Pse-AAC)

  • Z-scales

  • MSWHIM

  • Vectors of hydrophobic, steric and electronic properties (VHSE)

  • FASGAI

  • ProtFP

 [36, 82–84, 86]
Similarity measures

  • Sequence based:

    • BLOSUM/PAM substitution matrix

    • Needleman–Wunsch Score

    • Normalized Smith–Waterman Score

    • Position-specific scoring matrix (PSSM)

    • Substitution matrix representation (SMR)

  • Structure based: Global alignment scores

    • RMSD score

    • GDT score

    • MaxSub score

    • TM ccore

  • Local alignment scores

    • GA score

    • Match score

    • eMatchSite score

    • PS score

  • Ontological annotation semantic similarity

 [36, 86–91]
Topological properties

  • T-scales

  • ST-scales

 [36, 84]
Geometrical characteristics

  • Residue–residue contacts

  • Local descriptors of protein structure (LDPS)

  • Bond lengths, bond angles and dihedral angles

  • Secondary structure prediction

  • B-factor and disordered residues

  • Solvent accessible surface area

 [86, 88, 92, 93]
Functional sites

  • Protein domain profiles

  • Binding pockets and cavities

    • FuzCav

    • FLAP

 [83, 84, 94, 95]