Using convex hulls to extract interaction interfaces from known structures

Dafas, Panos; Bolser, Dan; Gomoluch, Jacek; Park, Jong; Schroeder, Michael

doi:10.1093/bioinformatics/bth106

Cited by 21 publications

(14 citation statements)

References 4 publications

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“…InterPare, at the time of this writing, contains 26,999 PDB entries (September 2004). At present, there is a faster algorithm available that uses the convex hull concept [36]. However, the present C program was efficient enough in that it took only 15 hours to complete the calculation for all the entries in the PDB.…”

Section: Construction and Contentmentioning

confidence: 99%

A protein domain interaction interface database: InterPare

et al. 2005

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Background: Most proteins function by interacting with other molecules. Their interaction interfaces are highly conserved throughout evolution to avoid undesirable interactions that lead to fatal disorders in cells. Rational drug discovery includes computational methods to identify the interaction sites of lead compounds to the target molecules. Identifying and classifying protein interaction interfaces on a large scale can help researchers discover drug targets more efficiently.

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Section: Construction and Contentmentioning

confidence: 99%

A protein domain interaction interface database: InterPare

et al. 2005

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“…Shown in the figure is the mid-surface between the two chains and called an interaction interface. Note that many of the important phenomena in proteins are mediated by this kind of molecular interface between proteins and proteins with small molecules called ligands [4]. For example, see Fig.…”

Section: Applications To Protein Structure Analysismentioning

confidence: 99%

Euclidean Voronoi diagrams of 3D spheres and applications to protein structure analysis

Kim

Cho

Kim

et al. 2005

Japan J. Indust. Appl. Math.

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Despite its many important applications in various disciplines in sciences and engineering, the Euclidean Voronoi diagram for spheres in 3D space has not been studied as much as it deserves. In this paper, we present an algorithm to compute a Euclidean Voronoi diagram for 3D spheres and show how the diagram can be used in the analysis of protein structures.Given an initial Voronoi vertex, the presented edge-tracing algorithm follows Voronoi edges until the construction is completed in O(mn) time in the worst-case, where m and n are the numbers of edges and spheres, respectively.Once a Voronoi diagram for 3D atoms of a protein is computed, it is shown that the diagram can be used to efficiently and precisely analyze the spatial structure of the protein. It turns out that this capability of a Voronoi diagram can be crucial to solving several important problems remaining to be solved in structural biology.

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“…There are three different methods to do this: Full Atom Contact (FAC); Sample Atom Contact (SAC); and Bounding Box Contact (BBC). FAC is the most accurate, whereas SAC and BBC [Dafas et al 2004] are faster methods.…”

Section: Protein Structural Interactome Map -Psimapmentioning

confidence: 99%