Open AccessAutomated ligand placement and refinement with a combined force field and shape potential
Author(s) -
Wlodek S.,
Skillman A. G.,
Nicholls A.
Publication year - 2006
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444906016076
Subject(s) - force field (fiction) , gaussian , adiabatic process , set (abstract data type) , field (mathematics) , computer science , series (stratigraphy) , potential energy , ligand (biochemistry) , algorithm , computational science , statistical physics , computational chemistry , physics , mathematics , classical mechanics , chemistry , artificial intelligence , pure mathematics , thermodynamics , paleontology , receptor , biology , programming language , biochemistry
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.