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Bioinformatics Advance Access originally published online on March 27, 2006
Bioinformatics 2006 22(12):1449-1455; doi:10.1093/bioinformatics/btl115
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

GBPM: GRID-based pharmacophore model: concept and application studies to protein–protein recognition

Francesco Ortuso 1, Thierry Langer 2 and Stefano Alcaro 1,*

1 Dipartimento di Scienze Farmacobiologiche Università di Catanzaro ‘Magna Græcia’ Complesso Ninì Barbieri I-88021, Roccelletta di Borgia (CZ), Italy
2 Institute of Pharmacy, Department of Pharmaceutical Chemistry Innrain 52a, University of Innsbruck, A-6020 Innsbruck, Austria

*To whom correspondence should be addressed.

Motivation: Automatic procedures to obtain pharmacophore models from experimentally determined macromolecular complexes can help in the drug discovery process, especially when protein–protein recognition plays an important biological role.

Results: The GRID-based pharmacophore model (GBPM) is a fully objective method for defining most relevant interaction areas in complexes deriving pharmacophore models from three-dimensional (3D) molecular structure information. It is based on logical and clustering operations with 3D maps computed by the GRID program on structurally known molecular complexes. In this manuscript we describe the concept and discuss application examples regarding protein–protein recognition. In particular two complexes selected in the Protein Data Bank have been tested to evaluate the GBPM capability to identify interaction areas. The results obtained show the capabilities of this new bioinformatic method.

Availability: The GBPM method has not been developed as a new computational code. It is based on the combination of existing scientific programs.

Contact: alcaro{at}unicz.it

Received on January 30, 2006; revised on March 3, 2006; accepted on March 22, 2006

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