GPU-based detection of protein cavities using Gaussian surfaces
作者: Sérgio E. D. DiasAna Mafalda MartinsQuoc T. NguyenAbel J. P. Gomes
作者单位: 1Universidade da Beira Interior
2Instituto de Telecomunicações
刊名: BMC Bioinformatics, 2017, Vol.18 (1)
来源数据库: Springer Journal
DOI: 10.1186/s12859-017-1913-4
关键词: GaussianFinderCavity detectionPocket detectionGaussian kernel function
英文摘要: Protein cavities play a key role in biomolecular recognition and function, particularly in protein-ligand interactions, as usual in drug discovery and design. Grid-based cavity detection methods aim at finding cavities as aggregates of grid nodes outside the molecule, under the condition that such cavities are bracketed by nodes on the molecule surface along a set of directions (not necessarily aligned with coordinate axes). Therefore, these methods are sensitive to scanning directions, a problem that we call cavity ground-and-walls ambiguity, i.e., they depend on the position and orientation of the protein in the discretized domain. Also, it is hard to distinguish grid nodes belonging to protein cavities amongst all those outside the protein, a problem that we call cavity ceiling...
原始语种摘要: Protein cavities play a key role in biomolecular recognition and function, particularly in protein-ligand interactions, as usual in drug discovery and design. Grid-based cavity detection methods aim at finding cavities as aggregates of grid nodes outside the molecule, under the condition that such cavities are bracketed by nodes on the molecule surface along a set of directions (not necessarily aligned with coordinate axes). Therefore, these methods are sensitive to scanning directions, a problem that we call cavity ground-and-walls ambiguity, i.e., they depend on the position and orientation of the protein in the discretized domain. Also, it is hard to distinguish grid nodes belonging to protein cavities amongst all those outside the protein, a problem that we call cavity ceiling...
全文获取路径: Springer  (合作)
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影响因子:3.024 (2012)

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关键词翻译
关键词翻译
  • protein 蛋白质
  • detection 探测
  • directions 指示
  • kernel 
  • orientation 定向
  • outside 外边
  • recognition 识别
  • cavity 
  • coordinate 坐标
  • necessarily 必定