CYPSI
Computational Tool
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General Information
DescriptionA structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana
Homepagehttp://bioinfo.cau.edu.cn/CYPSI
Publications
CYPSI: a structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana
Gaihua Zhang; Yijing Zhang; Zhen Su
Background The cytochrome P450 (CYP) superfamily enables terrestrial plants to adapt to harsh environments. CYPs are key enzymes involved in a wide range of metabolic pathways. It is particularly useful to be able to analyse the three-dimensional (3D) structure when investigating the interactions between CYPs and their substrates. However, only two plant CYP structures have been resolved. In addition, no currently available databases contain structural information on plant CYPs and ligands. Fortunately, the 3D structure of CYPs is highly conserved and this has made it possible to obtain structural information from template-based modelling (TBM).
Description The CYP Structure Interface (CYPSI) is a platform for CYP studies. CYPSI integrated the 3D structures for 266 CYPs predicted by three TBM methods: BMCD, which we developed specifically for CYP TBM; and two well-known web-servers, MUSTER and I-TASSER. After careful template selection and optimization, the models built by BMCD were accurate enough for practical application, which we demonstrated using a docking example aimed at searching for the CYPs responsible for ABA 8-hydroxylation. CYPSI also provides extensive resources for CYP structure and function studies, including 400 PDB entries for solved CYPs, 48 metabolic pathways associated with CYPs, 232 reported CYP ligands and 18 CYPs docked with ligands (61 complexes in total). In addition, CYPSI also includes the ability to search for similar sequences and chemicals.
Conclusions CYPSI provides comprehensive structure and function information for CYPs, which should facilitate investigations into the interactions between CYPs and their substrates. CYPSI has a user-friendly interface, which is available athttp://bioinfo.cau.edu.cn/CYPSI.
DOI: https://doi.org/10.1186/1471-2105-13-332
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