Homology Modeling and Docking of D1 Protein

The target D1 protein of A. adenophora can be provided on the basis of the amino acid sequence (reference sequence no. YP 004564352.1). The sequence of amino acid was obtained from NCBI, in FASTA format. Evolutionary related protein structures were searched for by the BLAST databases through the SWISS-MODEL Template Library (SMTL) [53 (link)]. Searched templates of D1 protein were estimated using Global Model Quality Estimate (GMQE) and Quaternary Structure Quality Estimate (QSQE) and ranked by the expected quality of the resulting models. The protein structures of top-ranked templates were selected from the Protein Data Bank (PDB) and built the homology model of A. adenophora D1 protein by the Protein Module of Discovery Studio. The chemical structure of CA was constructed with the software of ChemBioDraw Ultra 14.0 (CambridgeSoft, Cambridge, MA, USA), and the Chem3D Pro 14.0 (CambridgeSoft, Cambridge, MA, USA) was used to minimize energy. The docking was performed by DS-CDocker in Discovery Studio 2016 (BIOVIA, San Diego, CA, USA). The polar was added to the protein during energy minimization and molecular refinement.