Computational Geometry and Proteins – Københavns Universitet

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Datalogisk Institut, DIKU > Forskning > Algorithms and Programming Languages (APL) > Computational Biology > Computational Geometry...

Computational Geometry and Proteins

Adjustable Chain Trees

A modified version of chain trees that adjust themselves to the changing conformations of folding proteins is introduced. Computational results indicate that the number of intersection checks of bounding volumes is substantially reduced both in connection with the clash tests and the free energy calculations.

Pawel Winter and Rasmus Fonseca
Adjustable Chain Trees for Proteins
to appear in the Journal of Computational Biology


Protein Packing Quality Using Delaunay Complexes

Rasmus Fonseca, Pawel Winter and Kevin Karplus
Protein Packing Quality Using Delaunay Complexes
Proc. of 8-th Int. Symp. on Voronoi Diagrams in Science and Engineering, ISVD'11, Qingdao, China (2011)

Alpha Shapes and Proteins

Abstract: We provide a unified description of (weighted) alpha-shapes, beta-shapes and the corresponding simplicial complexes. We discuss their applicability to various protein-related problems. We also discuss filtrations of alpha-shapes and touch upon related persistence issues. We claim that the full potential of alpha-shapes and related geometrical constructs in protein-related problems yet remains to be realized and verified. We suggest parallel algorithms for (weighted) alpha-shapes, and we argue that future use of filtrations and kinetic variants for larger proteins will need such implementations.

Pawel Winter, Henrik Sterner and Peter Sterner
Alpha shapes and proteins
Proc. of 6-th Int. Symp. on Voronoi Diagrams in Science and Engineering, ISVD'09, Lyngby, Denmark (2009) 217-224

Henrik Sterner and Peter Sterner
Parallel alpha-forms in theory and practice (in Danish)
Master Thesis, Dept. of Computer Science, Univ. of Copenhagen (2008)