An accelerated pocket extraction and evaluation technique for druggability analysis with protein surfaces

Nakamura, Yukari; Kaneko, Ayaka; Itoh, Takayuki

doi:10.1145/2073304.2073338

Cited by 5 publications

(4 citation statements)

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“…In the experiments introduced in this section, we extracted pockets by a quick pocket extraction technique [4] applied on protein surface data, searched for non-protein atoms/molecules around the extracted pockets, and finally determined the reactivity of the pockets.…”

Section: Resultsmentioning

confidence: 99%

“…Our implementation extracts pockets from the protein surface datasets by applying a quick extraction technique [4]. This technique goes through the following procedures, and extracts pockets from protein surfaces.…”

Section: B Pocket Extractionmentioning

confidence: 99%

“…We proposed a technique for pocket extraction from protein surfaces [4], which requires less computation time than the existing techniques. This technique enables extracting appropriate concave portions of the protein surfaces; however, the extracted pockets are not necessarily druggable.…”

Section: Introductionmentioning

confidence: 99%

“…First, our technique uses protein surface datasets downloaded from the protein surface database "eFsite" [8]. Then we extracted pockets from the dataset applying a quick extraction technique [4]. Next, we calculated the geometric features of the pockets.…”

Section: Introductionmentioning

confidence: 99%

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A Visual Analytics of Geometric Distances between Amino Acids and Surface Pockets of Proteins

Makiko

Kaneko

Itoh

et al. 2014

2014 18th International Conference on Information Visualisation

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Abstract-Protein is the major component of the organism. It has a unique three-dimensional structure formed by its amino acid sequence. A concave (pocket) on the surface of a protein is known to be the best target for a drug to react. We started analyzing how "druggability" of proteins related to the location of amino acids in a pocket. This paper presents a visualization tool for distance analysis between pockets and the amino acid residue. Provided that a protein surface is described by a triangular mesh, this tool first identifies pockets on the protein surface, specifies the deepest point and outer loops of the pocket, and calculates distances between atoms of an amino acid residue and the deepest point or the outer loops of the pocket. The tool then visualizes the statistics of the distance calculation results by polyline charts and the distribution by scatterplots. This paper proposes a biological interpretation of the visualization results.

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Section: Resultsmentioning

confidence: 99%

Section: B Pocket Extractionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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