A Comprehensive Docking Study on the Selectivity of Binding of Aromatic Compounds to Proteins

Csaba Hetényi, Uko Maran, Mati Karelson

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14 Citations (Scopus)


Generally, computer-aided drug design is focused on screening of ligand molecules for a single protein target. The screening of several proteins for a ligand is a relatively new application of molecular docking. In the present study, complexes from the Brookhaven Protein Databank were used to investigate a docking approach of protein screening. Automated molecular docking calculations were applied to reproduce 44 protein-aromatic ligand complexes (31 different proteins and 39 different ligand molecules) of the databank. All ligands were docked to all different protein targets in altogether 12 090 docking runs. Based on the results of the extensive docking simulations, two relative measures, the molecular interaction fingerprint (MIF) and the molecular affinity fingerprint (MAP), were introduced to describe the selectivity of aromatic ligands to different proteins. MIF and MAP patterns are in agreement with fragment and similarity considerations. Limitations and future extension of our approach are discussed.

Original languageEnglish
Pages (from-to)1576-1583
Number of pages8
JournalJournal of Chemical Information and Computer Sciences
Issue number5
Publication statusPublished - Sep 1 2003


ASJC Scopus subject areas

  • Chemistry(all)
  • Information Systems
  • Computer Science Applications
  • Computational Theory and Mathematics

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