Related Experiment Video
Updated: Aug 1, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
Published on: July 19, 2024
Automated ligand placement and refinement with a combined force field and shape potential
S Wlodek1, A G Skillman, A Nicholls
1OpenEye Scientific Software, 3600 Cerrillos Road, Santa Fe, NM 87507, USA. stan@eyesopen.com
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.
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