title: GAMESS as a free quantum-mechanical platform for drug research.
abstract: Driven by a steady improvement of computational hardware and significant progress in ab initio method development, quantum-mechanical approaches can now be applied to large biochemical systems and drug design. We review the methods implemented in GAMESS, which are suitable to calculate large biochemical systems. An emphasis is put on the fragment molecular orbital method (FMO) and quantum mechanics interfaced with molecular mechanics (QM/MM). The use of FMO in the protein-ligand binding, structure-activity relationship (SAR) studies, fragment- and structure-based drug design (FBDD/SBDD) is discussed in detail.
authors.affiliation: Argonne Leadership Computing Facility, Argonne National Laboratory, 9700 South Cass Avenue, Building 240, Argonne, IL 60439, USA.
authors.forename: Yuri
authors.initials: Y
authors.lastname: Alexeev
authors.forename: Michael P
authors.initials: MP
authors.lastname: Mazanetz
authors.forename: Osamu
authors.initials: O
authors.lastname: Ichihara
authors.forename: Dmitri G
authors.initials: DG
authors.lastname: Fedorov
mesh_terms: D019295:Computational Biology / Q000379:methods; D015195:Drug Design; D055808:Drug Discovery / Q000379:methods; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D011789:Quantum Theory; D012984:Software
chemical_list: D008024:Ligands