The Influence of Structure Representation on QSAR Modelling

  • Marjana Novič
  • Matevž Pompe
  • Jure Zupan


In all kinds of QSAR studies it is very important how the chemical structure is represented. Usually a set of structural properties, calculated or extracted experimentally, is considered as a structure representation vector when compared and correlated to a biological property. Numerous attempts to suggest different structure representations reflect the vital importance of the structural coding problem in all kind of modelling procedures. Just a few examples are given for illustration in references1–7. One possible way of representing structures is by using a complete 3D structure information — atom type and coordinates. However, this representation suffers primarily from the lack of uniformity. Molecules containing different number of atoms N yield representations of matrices of various size (N×3 or N×4). Molecular descriptors originating from graph theory overcome the uniformity problem, they are also suitable because of their simplicity and often show good correlation with molecular properties8 but the 3-D structural properties of compounds are lost. With the new “spectrum-like” structure code developed by Zupan et al.6,7 the 3D representation is uniform, unique and reversible.


Multiple Linear Regression Structure Representation Multiple Linear Regression Model Molecular Descriptor Mulliken Charge 
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Copyright information

© Springer Science+Business Media New York 2000

Authors and Affiliations

  • Marjana Novič
    • 1
  • Matevž Pompe
    • 2
  • Jure Zupan
    • 1
  1. 1.National Institute of ChemistryLjubljanaSlovenia
  2. 2.Faculty of Chemistry and Chemical TechnologyUniversity of LjubljanaLjubljanaSlovenia

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