title: LiGen: a high performance workflow for chemistry driven de novo design.
abstract: Tools for molecular de novo design are actively sought incorporating sets of chemical rules for fast and efficient identification of structurally new chemotypes endowed with a desired set of biological properties. In this paper, we present LiGen, a suite of programs which can be used sequentially or as stand-alone tools for specific purposes. In its standard application, LiGen modules are used to define input constraints, either structure-based, through active site identification, or ligand-based, through pharmacophore definition, to docking and to de novo generation. Alternatively, individual modules can be combined in a user-defined manner to generate project-centric workflows. Specific features of LiGen are the use of a pharmacophore-based docking procedure which allows flexible docking without conformer enumeration and accurate and flexible reactant mapping coupled with reactant tagging through substructure searching. The full description of LiGen functionalities is presented.
authors.affiliation: Dompé R&D Centre, Dompé SpA, Via Campo di Pile, 67100 L'Aquila, Italy. a.beccari@dompe.it
authors.forename: Andrea R
authors.initials: AR
authors.lastname: Beccari
authors.forename: Carlo
authors.initials: C
authors.lastname: Cavazzoni
authors.forename: Claudia
authors.initials: C
authors.lastname: Beato
authors.forename: Gabriele
authors.initials: G
authors.lastname: Costantino
mesh_terms: D015195:Drug Design; D008024:Ligands; D062105:Molecular Docking Simulation; D012984:Software; D057188:Workflow
chemical_list: D008024:Ligands