Drug Design 2 - Applied Bioinformatics Group
Drug Design 2 - Applied Bioinformatics Group
Drug Design 2 - Applied Bioinformatics Group
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Topological Indices<br />
• There is a whole range of addi%onal topological indices that have<br />
been applied successfully<br />
• Topological indices are usually easy to compute<br />
• Calcula%on is omen based on the distance matrix of the molecular<br />
graph<br />
• A disadvantage of topological indices is that they are unrelated to<br />
observable physical quanDDes<br />
• They are par%cularly suitable, if proper%es like shape or degree of<br />
branching are expected to have an influence on the property<br />
predicted<br />
• Other physical quan%%es (e.g., hydrophobicity, electrosta%c<br />
proper%es) can be easily combined with topological indices<br />
3D Descriptors<br />
• 3D descriptors also consider molecular geometries<br />
• They are typically based on a selected, energy-‐minimized<br />
conforma%on<br />
• Choice of this conformaDon has a significant influence on the<br />
descriptor values!<br />
• 3D descriptors consider for example<br />
• Intramolecular distances<br />
• Bond lengths<br />
• Shape and size of the structure<br />
• Molecular surface areas<br />
• ...<br />
• They may consider the geometry alone, but omen also the<br />
distribu%on of proper%es with respect to the geometry (e.g.,<br />
polarity of a surface)<br />
3D Descriptors – RDF<br />
• The distribu%on of all intramolecular distances is captured<br />
by the radial distribuDon funcDon (RDF)<br />
• Because the distances are typically discrete, they are turned<br />
into a density funcDon:<br />
B is a constant describing the width of the Gaussian<br />
contribu%on to the density func%on<br />
• RDF is a one-‐dimensional descripDon of the three-‐<br />
dimensional geometry of a molecule
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