LigandScout
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LigandScout is computer software that allows creating three-dimensional (3D) pharmacophore models from structural data of macromolecule–ligand complexes, or from training and test sets of organic molecules. It incorporates a complete definition of 3D chemical features (such as hydrogen bond donors, acceptors, lipophilic areas, positively and negatively ionizable chemical groups) that describe the interaction of a bound small organic molecule (ligand) and the surrounding binding site of the macromolecule.[1] These pharmacophores can be overlaid and superimposed using a pattern-matching based alignment algorithm[2] that is solely based on pharmacophoric feature points instead of chemical structure. From such an overlay, shared features can be interpolated to create a so-called shared-feature pharmacophore that shares all common interactions of several binding sites/ligands or extended to create a so-called merged-feature pharmacophore. The software has been successfully used to predict new lead structures in drug design, e.g., predicting biological activity of novel human immunodeficiency virus (HIV) reverse transcriptase inhibitors.[3]
Similar tools
Other software tools which help to model pharmacophores include:
- Molecular Operating Environment] (MOE) – by the Chemical Computing Group[4]
- Phase – by Schrödinger[5]
- Discovery Studio – by Accelrys[6]
- SYBYL-X – by Tripos[7]
- Pharao by Silicos-It[1]
See also
References
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Further reading
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