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Updated: Aug 18, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Quality of approximate electron densities and internal consistency of molecular alignment algorithms in molecular
Patrick Bultinck1, Ramon Carbó-Dorca, Christian Van Alsenoy
1Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S-3), B-9000 Gent, Belgium. Patrick.Bultinck@UGent.be
Abstract:
The calculation of molecular quantum similarity measures using the molecular electron density requires the electron density and molecular alignment between two molecules. To obtain meaningful quantum similarity matrices, the electron density should be calculated efficiently and accurately and the alignment should be internally consistent. The internal consistency of the alignment for a series of molecules is investigated through distance geometry concepts. The calculation of the quantum similarity matrix requires the calculation of a quadratic number of similarity integrals, and a scheme to obtain these efficiently is developed. Both the alignment procedure and the ASA method for approximate molecular electron densities are tested for a set of steroid molecules.
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