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Acta Crystallogr D Struct Biol. 2017 Mar 1;73(Pt 3):195-202. doi: 10.1107/S2059798317003400. Epub 2017 Mar 6.

Estimation of the protein-ligand interaction energy for model building and validation.

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European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany.


Macromolecular X-ray crystallography is one of the main experimental techniques to visualize protein-ligand interactions. The high complexity of the ligand universe, however, has delayed the development of efficient methods for the automated identification, fitting and validation of ligands in their electron-density clusters. The identification and fitting are primarily based on the density itself and do not take into account the protein environment, which is a step that is only taken during the validation of the proposed binding mode. Here, a new approach, based on the estimation of the major energetic terms of protein-ligand interaction, is introduced for the automated identification of crystallographic ligands in the indicated binding site with ARP/wARP. The applicability of the method to the validation of protein-ligand models from the Protein Data Bank is demonstrated by the detection of models that are `questionable' and the pinpointing of unfavourable interatomic contacts.


ARP/wARP; LigEnergy; automated identification of crystallographic ligands; protein–ligand interaction energy; protein–ligand interactions; structure validation

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