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Updated: Feb 23, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Neighboring Structure Visualization on a Grid-based Layout
G Marcou1, D Horvath1, A Varnek1
1Laboratory of Chemoinformatics, University of Strasbourg, 1 rue Biaise Pascal, 67000, Strasbourg, France.
Abstract:
Here, we describe an algorithm to visualize chemical structures on a grid-based layout in such a way that similar structures are neighboring. It is based on structure reordering with the help of the Hilbert Schmidt Independence Criterion, representing an empirical estimate of the Hilbert-Schmidt norm of the cross-covariance operator. The method can be applied to any layout of bi- or three-dimensional shape. The approach is demonstrated on a set of dopamine D5 ligands visualized on squared, disk and spherical layouts.
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