Automated Ligand Placement and Refinement with a Combined Force Field and Shape Potential.
From: OpenEye Scientific Software, 3600 Cerrillos Road, Santa Fe, NM 87507, USA. stan@eyesopen.com
Acta crystallographica. Section D, Biological crystallography
- Publish Date: Jul 2006
- ISSN: 0907-4449
- Volume: 62
- Issue: Pt 7
- Pages: 741-9
- Medium: Print
- Language: English
- Citation (JAMA): Wlodek S, Skillman A G, Nicholls A, et al. Automated Ligand Placement and Refinement with a Combined Force Field and Shape Potential.. Acta Crystallogr. D Biol. Crystallogr. Jul 2006;62:741-9
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.
Mesh Headings (Keywords): Algorithms, Binding Sites, Computer Simulation, Crystallography, X-Ray, Hydrogen Bonding, Ligands, Models, Molecular, Molecular Conformation, Molecular Structure, Protein Binding, Proteins, Structure-Activity Relationship, Thermodynamics
Check for Full Text / PubMed Unique Identifier (PMID): 16790930
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