PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins.

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ID: 171927
2020
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Abstract
Heme participates in a wide range of biological functions such as oxygen transport, electron transport, oxygen reduction, transcriptional regulation and so on. While the mechanism of each function has been investigated for many heme proteins, the origin of the diversity of the heme functions is still unclear and a crucial scientific issue. We have constructed a database of heme proteins, named Python-based database and analyzer for DIStortion of Heme porphyrin (PyDISH), which also contains some analysis tools. The aim of PyDISH is to integrate the information on the structures of hemes and heme proteins and the functions of heme proteins. This database will provide the structure-function relationships focusing on heme porphyrin distortion and lead to the elucidation of the origin of the functional diversity of heme proteins. In addition, the insights obtained from the database can be used for the design of protein function. PyDISH contains the structural data of more than 13 000 hemes extracted from the Protein Data Bank, including heme porphyrin distortion, axial ligands coordinating to the heme and the orientation of the propionate sidechains of heme. PyDISH also has information about the protein domains, including Uniprot ID, protein fold by CATH ID, organism, coordination distance and so on. The analytical tools implemented in PyDISH allow users to not only browse and download the data but also analyze the structures of heme porphyrin by using the analytical tools implemented in PyDISH. PyDISH users will be able to utilize the obtained results for the design of protein function. Database URL: http://pydish.bio.info.hiroshima-cu.ac.jp/.
Reference Key
kondo2020pydishdatabase Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Kondo, Hiroko X;Kanematsu, Yusuke;Masumoto, Gen;Takano, Yu;
Journal Database : the journal of biological databases and curation
Year 2020
DOI
baaa066
URL
Keywords
structural elucidation mapk cytotoxic activity apiaceae ferula sinkiangensis k.m.shen sesquiterpene coumarin

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