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. 2018 May 4:43–73. doi: 10.1016/B978-0-12-812364-5.00002-X

Table 2.2.

Uses and Tools and/or Algorithms Important in Computational Methods of Herbal Medicine

Methods Prerequisites Use Tools/Algorithms
Ligand-based screening Knowledge of compounds with known activity To identify putatively active compounds Classification/regression trees (including Random Forest), linear discriminant analysis, artificial neural networks, support vector machines
Pharmacophore (ligand-based or target-based)
  • •

    3D structures of known ligands to chosen targets

    (Ligand-based)

  • •

    known 3D structures of target protein(s)

    ideally known as

    3D structure(s) of known complex(es) (Target-based)

 To identify putative active compounds LigandScout, Schrödinger’s Phase program, Accelrys’s Discovery Studio Catalyst, etc.
Docking Known 3D structure (s) of target proteins To ‘dock’ potential small molecule ligands into protein active sites, optimizing their topographical and chemical complementarity, and scoring their interaction FlexX, Gold, Dock, Glide, MolDock, AutoDock, LigandFit, etc.
Pattern recognition Post-screening analyses (involving dimensionality reduction) Principle components analysis (PCA), multidimensional scaling, self-organizing maps, various forms of cluster analysis, etc.
Proteomics and genomics data visualization and analysis Application-specific programs for statistical processing and visualization of data output from DNA micro-array experiments, MS proteomics experiments, etc.