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Figure 1
The process involved in generating a ligand description and conformer generation using CCP4/AceDRG. From an input SMILES string, the first step is to create a graphical representation of the ligand using AceDRG/RDKit, which encodes basic chemical properties and interactions. This can be depicted in two dimensions and edited using Lidia. A full ligand description is generated, with reference to prior knowledge specifying details of the restraints for bond lengths, angles, torsions etc., using AceDRG. Using these restraints, RDKit generates an initial three-dimensional conformer before REFMAC5 is executed to optimize the coordinates.

Journal logoSTRUCTURAL
ISSN: 2059-7983
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