Protein packing quality using Delaunay complexes

TY - GEN

T1 - Protein packing quality using Delaunay complexes

AU - Fonseca, Rasmus

AU - Winter, Pawel

AU - Karplus, Kevin

N1 - Conference code: 8

PY - 2011

Y1 - 2011

N2 - A new method for estimating the packing quality of protein structures is presented. Atoms in high quality protein crystal structures are very uniformly distributed which is difficult to reproduce using structure prediction methods. Packing quality measures can therefore be used to assess structures of low quality and even to refine them. Previous methods mainly use the Voronoi cells of atoms to assess packing quality. The presented method uses only the lengths of edges in the Delaunay complex which is faster to compute since volumes of Voronoi cells are not evaluated explicitly. This is a novel application of the Delaunay complex that can improve the speed of packing quality computations. Doing so is an important step for, e.g., integrating packing measures into structure refinement methods. High- and low-resolution X-ray crystal structures were chosen to represent well- and poorly-packed structures respectively. Our results show that the developed method is correlated to the well-established RosettaHoles2 but three times faster.

AB - A new method for estimating the packing quality of protein structures is presented. Atoms in high quality protein crystal structures are very uniformly distributed which is difficult to reproduce using structure prediction methods. Packing quality measures can therefore be used to assess structures of low quality and even to refine them. Previous methods mainly use the Voronoi cells of atoms to assess packing quality. The presented method uses only the lengths of edges in the Delaunay complex which is faster to compute since volumes of Voronoi cells are not evaluated explicitly. This is a novel application of the Delaunay complex that can improve the speed of packing quality computations. Doing so is an important step for, e.g., integrating packing measures into structure refinement methods. High- and low-resolution X-ray crystal structures were chosen to represent well- and poorly-packed structures respectively. Our results show that the developed method is correlated to the well-established RosettaHoles2 but three times faster.

KW - Faculty of Science

KW - proteins

KW - Packing quality

KW - Delaunay complex

U2 - 10.1109/ISVD.2011.23

DO - 10.1109/ISVD.2011.23

M3 - Article in proceedings

SN - 978-0-7695-4483-0

SP - 117

EP - 122

BT - Eigth International Symposium on Voronoi Diagrams in Science and Engineering

A2 - Anton, Francois

A2 - Wang, Wenping

PB - IEEE

T2 - 8th International Symposium on Voronoi Diagrams in Science and Engineering

Y2 - 28 June 2011 through 30 June 2011

ER -