Power diagrams: properties, algorithms and applications
SIAM Journal on Computing
Three-dimensional alpha shapes
ACM Transactions on Graphics (TOG)
Defining, Computing, and Visualizing Molecular Interfaces
VIS '95 Proceedings of the 6th conference on Visualization '95
Interface surfaces for protein-protein complexes
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Analysis of Protein Protein Dimeric Interfaces
BIBM '07 Proceedings of the 2007 IEEE International Conference on Bioinformatics and Biomedicine
Bioinformatics
Interaction interfaces in proteins via the Voronoi diagram of atoms
Computer-Aided Design
Comparing Voronoi and Laguerre Tessellations in the Protein-Protein Docking Context
ISVD '09 Proceedings of the 2009 Sixth International Symposium on Voronoi Diagrams
Bioinformatics
Decomposition of a Protein Solution into Voronoi Shells and Delaunay Layers
ISVD '12 Proceedings of the 2012 Ninth International Symposium on Voronoi Diagrams in Science and Engineering
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The ability to analyze and compare protein-nucleic acid and protein-protein interaction interface has critical importance in understanding the biological function and essential processes occurring in the cells. Since high-resolution three-dimensional (3D) structures of biomacromolecule complexes are available, computational characterizing of the interface geometry become an important research topic in the field of molecular biology. In this study, the interfaces of a set of 180 protein-nucleic acid and protein-protein complexes are computed to understand the principles of their interactions. The weighted Voronoi diagram of the atoms and the Alpha complex has provided an accurate description of the interface atoms. Our method is implemented in the presence and absence of water molecules. A comparison among the three types of interaction interfaces show that RNA-protein complexes have the largest size of an interface. The results show a high correlation coefficient between our method and the PISA server in the presence and absence of water molecules in the Voronoi model and the traditional model based on solvent accessibility and the high validation parameters in comparison to the classical model.