The CYPSI frame. The raw data are shown in light blue; the processed data are shown in blue; the utilized tools are shown in green and the data resources are shown in red. The BMCD pipeline for CYP structure modelling was developed as part of this study. “Arabidopsis CYPs”: the A. thaliana CYP sequences. “CYPs structures”: the solved CYP structures. “Templates”: the structures recommended as templates for BMCD. “Prediction Structures” were generated by BMCD, I-TASSER and MUSTER. Metabolic “Pathways” were obtained from the PMN database and relevant scientific literature. “Ligands” were collected from “PubChem” or built manually. “Sequences” include the protein sequences of the A. thaliana CYPs and solved CYPs. The “Docked Complexes” were generated by CDOCKER software. In addition, BLAST for sequence alignment and ChemmineR for identifying chemicals with similar structures could be used to discover the relationships between CYPs and ligands.
Zhang et al. BMC Bioinformatics 2012 13:332 doi:10.1186/1471-2105-13-332