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bioRxiv · 10.1101/2022.01.24.468575

Observing noncovalent interactions in experimental electron density for macromolecular systems: A novel perspective for protein-ligand interaction research

Ding, K.·Yin, S.·Li, Z.·Jiang, S.·Yang, Y.·Zhou, W.·Huang, B.·Zhang, Y.
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Abstract

We report for the first time the use of experimental electron density (ED) in the Protein Data Bank for modeling non-covalent interactions (NCIs) for protein-ligand complexes. Our methodology is based on the reduced electron density gradient (RDG) theory describing intermolecular NCI by ED and its first derivative. We established a database called the Experimental NCI Database (ExptNCI; http://ncidatabase.stonewise.cn/#/nci) containing ED saddle points, indicating ~200,000 NCIs from over 12,000 protein-ligand complexes. We also demonstrated the use of the database for depicting amide-{pi} interactions in a protein-ligand binding system. In summary, the database provides details on experimentally observed NCIs for protein-ligand complexes and can support future studies, including studies on rarely documented NCIs and the development of artificial intelligent models for protein-ligand binding prediction.

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Ding, K., Yin, S., Li, Z., Jiang, S., Yang, Y., Zhou, W., Huang, B., Zhang, Y.. 2022-01-25. Observing noncovalent interactions in experimental electron density for macromolecular systems: A novel perspective for protein-ligand interaction research. https://doi.org/10.1101/2022.01.24.468575

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