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 [ edit ]

Other software tools which help to model pharmacophores include:

• Molecular Operating Environment] (MOE) ? by the Chemical Computing Group ^[4]
• Phase ? by Schrodinger ^[5]
• Discovery Studio ? by Accelrys ^[6]
• SYBYL-X ? by Tripos ^[7]
• Pharao by Silicos-It [1]

See also [ edit ]

• Comparison of software for molecular mechanics modeling

References [ edit ]

Further reading [ edit ]

• Wolber G, Kosara R (30 October 2006). "Chapter 6: Pharmacophores from Macromolecular Complexes with LigandScout". Pharmacophores and Pharmacophore Searches . Wiley. ISBN   3-527-31250-1 . Archived from the original on 2008-10-13.