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Bioinformatics Vol. 19 no. 16 2003
pages 2112-2121
© 2003 Oxford University Press

Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins

Kristian Rother , Robert Preissner , Andrean Goede and Cornelius Frömmel *

Berlin Center of Genome Based Bioinformatics (BCB), Humboldt University, Institute of Biochemistry at the Charite, Monbijoustr. 2, 10117 Berlin, Germany

Received on January 31, 2003 ; revised on April 30, 2003 ; accepted on May 20, 2003

Motivation: There is no consensus in the literature about how the deepest portions of protein structures are packed. Using an improved Voronoi procedure, we calculate reference packing densities for different regions in the protein interior. Furthermore, we want to clarify where cavities are located.

Results: Sets of reference packing densities are provided for regions in proteins that differ in their distance to the surface and to internal cavities, supplementing previous data. Packing in the protein interior is tight but generally inhomogeneous. There are about 4.4 cavities per 100 amino acids in protein structures, they occur in all regions, most frequently in a depth of 2.5–3.6 Å underneath the Connolly surface. However, the deepest protein regions have a lower mean packing density than circumjacent regions, because more contacts to cavities occur in the core.

Availability/Supplementary information: Calculation software and detailed packing data are available on request.

Contact: cornelius.froemmel{at}charite.de

* To whom correspondence should be addressed.


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