Journal of Computer-Aided Molecular Design

, Volume 29, Issue 3, pp 233–247

Continuous indicator fields: a novel universal type of molecular fields

  • Gleb V. Sitnikov
  • Nelly I. Zhokhova
  • Yury A. Ustynyuk
  • Alexandre Varnek
  • Igor I. Baskin
Article

Abstract

A novel type of molecular fields, Continuous Indicator Fields (CIFs), is suggested to provide 3D structural description of molecules. The values of CIFs are calculated as the degree to which a point with given 3D coordinates belongs to an atom of a certain type. They can be used similarly to standard physicochemical fields for building 3D structure–activity models. One can build CIF-based 3D structure–activity models in the framework of the continuous molecular fields approach described earlier (J Comput-Aided Mol Des 27 (5):427–442, 2013) for the case of physicochemical molecular fields. CIFs are thought to complement and further extend traditional physicochemical fields. The models built with CIFs can be interpreted in terms of preferable and undesirable positions of certain types of atoms in space. This helps to understand which changes in chemical structure should be made in order to design a compound possessing desirable properties. We have demonstrated that CIFs can be considered as 3D analogues of 2D topological molecular fragments. The performance of this approach is demonstrated in structure–activity studies of thrombin inhibitors, multidentate N-heterocyclic ligands for Am3+/Eu3+ separation, and coloring dyes.

Keywords

3D-QSAR Continuous molecular fields Kernel ridge regression Substructural approach Metal complexation Coloring dyes 

Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Gleb V. Sitnikov
    • 1
    • 4
  • Nelly I. Zhokhova
    • 2
  • Yury A. Ustynyuk
    • 3
  • Alexandre Varnek
    • 4
  • Igor I. Baskin
    • 2
    • 5
  1. 1.A.N.Nesmeyanov Institute of Organoelement Compounds of Russian Academy of SciencesMoscowRussia
  2. 2.Faculty of PhysicsM.V.Lomonosov Moscow State UniversityMoscowRussia
  3. 3.Department of ChemistryM.V.Lomonosov Moscow State UniversityMoscowRussia
  4. 4.Laboratoire de Chémoinformatique, UMR 7140 CNRSUniversité de StrasbourgStrasbourgFrance
  5. 5.Kazan (Volga River) Federal UniversityKazanRussia

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