ArticleDatabase : the journal of biological databases and curation2020
PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins.
Article in Database : the journal of biological databases and curation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Evaluation of AlphaFold3 for Predicting Human Heme-Binding Protein Structures.International journal of molecular sciences · 2026Article
- Advances in Computational Intelligence-Based Methods of Structure and Function Prediction of Proteins.Biomolecules · 2024Article
- Heme Spin Distribution in the Substrate-Free and Inhibited Novel CYP116B5hd: A Multifrequency Hyperfine Sublevel Correlation (HYSCORE) Study.Molecules (Basel, Switzerland) · 2024Article
- Computational Exploration of Minimum Energy Reaction Pathway of NInternational journal of molecular sciences · 2023Article
- Prediction of Protein Function from Tertiary Structure of the Active Site in Heme Proteins by Convolutional Neural Network.Biomolecules · 2023Article
- Elucidation of the Correlation between Heme Distortion and Tertiary Structure of the Heme-Binding Pocket Using a Convolutional Neural Network.Biomolecules · 2022Article
- Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications.International journal of molecular sciences · 2022Review
- Analysis of Fluctuation in the Heme-Binding Pocket and Heme Distortion in Hemoglobin and Myoglobin.Life (Basel, Switzerland) · 2022Article
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Authors and funding
4 authors.
Funding
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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/.
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Registered trials
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