title: AMMOS software: method and application.
abstract: Recent advances in computational sciences enabled extensive use of in silico methods in projects at the interface between chemistry and biology. Among them virtual ligand screening, a modern set of approaches, facilitates hit identification and lead optimization in drug discovery programs. Most of these approaches require the preparation of the libraries containing small organic molecules to be screened or a refinement of the virtual screening results. Here we present an overview of the open source AMMOS software, which is a platform performing an automatic procedure that allows for a structural generation and optimization of drug-like molecules in compound collections, as well as a structural refinement of protein-ligand complexes to assist in silico screening exercises.
authors.affiliation: Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria.
authors.forename: T
authors.initials: T
authors.lastname: Pencheva
authors.forename: D
authors.initials: D
authors.lastname: Lagorce
authors.forename: I
authors.initials: I
authors.lastname: Pajeva
authors.forename: B O
authors.initials: BO
authors.lastname: Villoutreix
authors.forename: M A
authors.initials: MA
authors.lastname: Miteva
mesh_terms: D001331:Automation; D019295:Computational Biology / Q000379:methods*; D004353:Drug Evaluation, Preclinical; D008968:Molecular Conformation; D011506:Proteins / Q000737:chemistry; D012984:Software
chemical_list: D011506:Proteins