title: VAMMPIRE: a matched molecular pairs database for structure-based drug design and optimization.
abstract: Structure-based optimization to improve the affinity of a lead compound is an established approach in drug discovery. Knowledge-based databases holding molecular replacements can be supportive in the optimization process. We introduce a strategy to relate the substitution effect within matched molecular pairs (MMPs) to the atom environment within the cocrystallized protein-ligand complex. Virtually Aligned Matched Molecular Pairs Including Receptor Environment (VAMMPIRE) database and the supplementary web interface ( http://vammpire.pharmchem.uni-frankfurt.de ) provide valuable information for structure-based lead optimization.
authors.affiliation: Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue Strasse 9, Frankfurt D-60438, Germany.
authors.forename: Julia
authors.initials: J
authors.lastname: Weber
authors.forename: Janosch
authors.initials: J
authors.lastname: Achenbach
authors.forename: Daniel
authors.initials: D
authors.lastname: Moser
authors.forename: Ewgenij
authors.initials: E
authors.lastname: Proschak
mesh_terms: D062313:Databases, Pharmaceutical; D015195:Drug Design; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D011506:Proteins / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D011506:Proteins