Computational protocol: Cinnamomum burmanini Blume increases bone turnover marker and induces tibia's granule formation in ovariectomized rats

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Protocol publication

[…] The compound structure of coumarin, eugenol, and trans-cinnamic acid (TCA) were obtained from a compound database of the National Center for Biotechnology Information (NCBI), United States National Library of Medicine (NLM), National Institutes of Health (NIH), and the protein sequences of RANK, RANKL, and OPG are NP_001258164.1; Q9ESE2.1; and O08727.1, respectively; retrieved from the sequence database of NCBI. Conversion *.sdf file of coumarin, eugenol, and TCA to become *.pdb file was done using Open Babel software , and modeling 3-D structure of RANK, RANKL, and OPG was predicted using the SWISS-MODEL web server , . Protein structure was analyzed by Ramachandran plot using RAMPAGE web server (http://mordred.bioc.cam.ac.uk). Interaction analysis by docking method analyzed by using HEX 6.12 software , . […]

Pipeline specifications

Software tools Open Babel, SWISS-MODEL
Applications Drug design, Protein structure analysis
Organisms Rattus norvegicus, Dipturus trachyderma
Diseases Bone Diseases, Osteoporosis, Xanthomatosis, Cerebrotendinous, Fractures, Bone
Chemicals Durapatite