Peng Tao1; Sun Lianying1; Zhou Jiaju2
Source Publication计算机与应用化学
AbstractVirtual screening is increasingly used as a cost-effective complement to high-throughput screening. And similarity methods play a key role in the ligand-based virtual screening approaches while the macromolecule structural information is unavailable. The Traditional Chinese Medicine Database was used to conduct hierarchical agglomerative clustering of effective compounds contained in TCM. There are many distance metrics and similarity coefficients commonly used in chemical information systems. In this paper, Daylight fingerprint was adopted as chemical structural representation method. And similarity indexes were calculated according to Tanimoto coefficient definition using the famous chemical library project-Chemical Development Kit (CDK). The hierarchical agglomerative clustering algorithm was implemented and conducted with the TCM database. And domain-specific knowledge was used to preprocess the molecules data in TCM database. The similarity threshold value of 0.75 was used in hierarchical agglomerative clustering of TCM database. The penalty value of Kelly method was calculated to get the optimal clusters number. And the clusters number calculated from Kelly method is very close to the clusters number resulted from hierarchical clustering using the threshold value of 0.75. Multiple representative molecules were calculated and selected from each non-singleton cluster. And the bias of Tanimoto coefficient was also analyzed. The scaffold analysis and scaffold-based clustering can be done in the future work.
Document Type期刊论文
Recommended Citation
GB/T 7714
Peng Tao,Sun Lianying,Zhou Jiaju. hierarchicalclusteringoftraditionalchinesemedicinedatabasebasedonmolecularfingerprint[J]. 计算机与应用化学,2013,30(6):575.
APA Peng Tao,Sun Lianying,&Zhou Jiaju.(2013).hierarchicalclusteringoftraditionalchinesemedicinedatabasebasedonmolecularfingerprint.计算机与应用化学,30(6),575.
MLA Peng Tao,et al."hierarchicalclusteringoftraditionalchinesemedicinedatabasebasedonmolecularfingerprint".计算机与应用化学 30.6(2013):575.
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