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Correction published on 18 March 2019, see Molecules 2019, 24(6), 1052.

Open AccessArticle

Ligand-Based Pharmacophore Modeling Using Novel 3D Pharmacophore Signatures

A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kremlevskaya Str. 18, 420008 Kazan, Russia
Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Hnevotinska 5, 77900 Olomouc, Czech Republic
Author to whom correspondence should be addressed.
Molecules 2018, 23(12), 3094;
Received: 6 November 2018 / Revised: 23 November 2018 / Accepted: 23 November 2018 / Published: 27 November 2018
(This article belongs to the Special Issue Computational Approaches for Drug Discovery)
PDF [5046 KB, uploaded 18 March 2019]


Pharmacophore modeling is a widely used strategy for finding new hit molecules. Since not all protein targets have available 3D structures, ligand-based approaches are still useful. Currently, there are just a few free ligand-based pharmacophore modeling tools, and these have a lot of restrictions, e.g., using a template molecule for alignment. We developed a new approach to 3D pharmacophore representation and matching which does not require pharmacophore alignment. This representation can be used to quickly find identical pharmacophores in a given set. Based on this representation, a 3D pharmacophore ligand-based modeling approach to search for pharmacophores which preferably match active compounds and do not match inactive ones was developed. The approach searches for 3D pharmacophore models starting from 2D structures of available active and inactive compounds. The implemented approach was successfully applied for several retrospective studies. The results were compared to a 2D similarity search, demonstrating some of the advantages of the developed 3D pharmacophore models. Also, the generated 3D pharmacophore models were able to match the 3D poses of known ligands from their protein-ligand complexes, confirming the validity of the models. The developed approach is available as an open-source software tool: and View Full-Text
Keywords: 3D pharmacophore signatures; 3D pharmacophore hash; pharmacophore modeling; ligand-based modeling 3D pharmacophore signatures; 3D pharmacophore hash; pharmacophore modeling; ligand-based modeling

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Kutlushina, A.; Khakimova, A.; Madzhidov, T.; Polishchuk, P. Ligand-Based Pharmacophore Modeling Using Novel 3D Pharmacophore Signatures. Molecules 2018, 23, 3094.

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