PMID: 8594163Oct 1, 1995Paper

The atom assignment problem in automated de novo drug design. 5. Tests for envelope-directed fragment placement based on molecular similarity

Journal of Computer-aided Molecular Design
M T Barakat, P M Dean

Abstract

The fragment placement method has been successfully extended to the problem of envelope-directed design. The atom assignment paradigm was based on molecular similarity between two molecular structures. A composite supersurface is defined to form the surface onto which the molecular fields are projected. The assignment process is then determined by using molecular similarity in the objective function to be optimized. In principle, this procedure is closely similar to that outlined in the previous paper for site-directed design. The rationale has been extensively tested on two benzodiazepine antagonists believed to bind to the same site.

References

Jun 1, 1995·Journal of Molecular Graphics·F E BlaneyR W Phippen
Aug 1, 1994·Journal of Computer-aided Molecular Design·R A Lewis, A R Leach
Apr 1, 1993·Journal of Computer-aided Molecular Design·T D Perkins, P M Dean
Aug 1, 1995·Journal of Computer-aided Molecular Design·M T Barakat, P M Dean
Aug 1, 1995·Journal of Computer-aided Molecular Design·M T Barakat, P M Dean
Aug 1, 1988·Journal of the American Chemical Society·R D CramerJ D Bunce

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Citations

Jul 19, 2000·Proteins·X FraderaJ Mestres
Oct 7, 2006·Journal of Molecular Modeling·Jordi Muñoz-MuriedasFrancisco Javier Luque
Jan 5, 2002·Journal of Molecular Graphics & Modelling·N E JewellG J Sexton
Apr 1, 1997·Journal of Molecular Graphics & Modelling·J MestresG M Maggiora
Aug 21, 2003·Drug Discovery Today·Giang Thanh LeWim Meutermans
Aug 14, 1999·Journal of Biomolecular Structure & Dynamics·B D SilvermanD E Platt
Dec 1, 1995·Journal of Computer-aided Molecular Design·C S Poornima, P M Dean
Aug 24, 2002·Pest Management Science·Jose L Martínez VidalEnrique López Carrique
Apr 12, 2002·Journal of Computational Chemistry·J MuñozF Javier Luque
Apr 14, 2015·Journal of Chemical Information and Modeling·Péter Englert, Péter Kovács
Jan 6, 2001·Journal of Molecular Graphics & Modelling·A R LeachA J Robinson

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