LigandScout

LigandScout is a software tool that allows to model 3D pharmacophore models from structural data of macromolecule/ligand complexes. It incorporates a complete definition of three-dimensional 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.cite journal |author=Wolber G, Langer T |title=LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters |journal=J Chem Inf Model |volume=45 |issue=1 |pages=160-169 |year=2005 |doi=10.1021/ci049885e] These pharmacophores can be overlaid and superimposed using a pattern-matching based alignment algorithmcite journal |author=Wolber G, Dornhofer AA, Langer T |title=Efficient overlay of small organic molecules using 3D pharmacophores |journal=J Comput Aided Mol Des |volume=20 |issue=12 |pages=773-788 |year=2007 |doi=10.1007/s10822-006-9078-7] 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. for the prediction of biological activity of novel HIV reverse transcriptase inhibitors.cite journal |author=Barreca ML, De Luca L, Iraci N, Rao A, Ferro S, Maga G, Chimirri A |title=Structure-based pharmacophore identification of new chemical scaffolds as non-nucleoside reverse transcriptase inhibitors |journal=J Chem Inf Model |volume=47 |issue=2 |pages=557-562 |year=2007 |doi=10.1021/ci600320q]

ee also

Other software tools which help to model pharmacophore include:
*Software for molecular mechanics modeling
* [http://www.chemcomp.com/ Molecular Operating Environment] (MOE) — by the Chemical Computing Group
* [http://www.schrodinger.com/ProductDescription.php?mID=6&sID=16 Phase] — by Schrödinger
* [http://accelrys.com/products/discovery-studio/ Discovery Studio] — by Accelrys

References

Further reading

* Pharmacophores from Macromolecular Complexes with LigandScout. Thierry Langer and Rémy D. Hoffmann (2006), editors, chapter 6 in "Pharmacophores and Pharmacophore Searches" ISBN 3-527-31250-1 [http://www.wiley.com/WileyCDA/WileyTitle/productCd-3527312501,descCd-tableOfContents.html Table of contents and preface]

External Links

* [http://www.inteligand.com/cgi-bin/ligandscout/manual.pl?file=/ligandscout/manual/introduction/index.html LigandScout manual and description of scientific applications] hosted by