title: Automated ligand placement and refinement with a combined force field and shape potential.
abstract: An automated computational procedure for fitting a ligand into its electron density with the use of the MMFF94 force field and a Gaussian shape description has been developed. It employs a series of adiabatic optimizations of gradually increasing shape potential. Starting from a set of energy-relaxed ligand conformations, the final results are structures realistically strained to fit the crystallographic data.
authors.affiliation: OpenEye Scientific Software, 3600 Cerrillos Road, Santa Fe, NM 87507, USA. stan@eyesopen.com
authors.forename: S
authors.initials: S
authors.lastname: Wlodek
authors.forename: A G
authors.initials: AG
authors.lastname: Skillman
authors.forename: A
authors.initials: A
authors.lastname: Nicholls
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D018360:Crystallography, X-Ray / Q000379:methods; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D015394:Molecular Structure; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D008024:Ligands; D011506:Proteins