2.2. Homology Modeling and Model Validation of UGT1A8

The homology modeling approach in the aid of Maestro (v 10.1, Schrödinger, LLC, New York, NY, 2015) was adopted to predict 3-D structure of the target protein human UGT1A8 for molecular docking analysis since it is not available until now. Firstly, the primary amino acid sequence was retrieved as a target from the NCBI database with an accession number of {"type":"entrez-protein","attrs":{"text":"Q9HAW9","term_id":"29839637","term_text":"Q9HAW9"}}Q9HAW9 and downloaded as a FAST ALL format file. Then BLAST (the program Basic Local Alignment Search Tool) was performed to find the best homologous sequence with known 3-D structure as template according to the alignment with target by pairwise comparison using BLOSUM62 matrix (Belhesda, LLC, Rockville, MA, USA). Based on the optimal template, homology model was generated with the automated protein structure homology-modeling server Prime Module using a default model. The homology model included copying backbone atom coordinates for aligned regions and side chains of conserved residues, loop modeling and optimization of side chains, building insertions and closing deletion in the alignment. After secondary structure predictions using the Prime module for alignment, the model was subjected to check for any missing side chain and all-atom ab initio energy minimization for refinement, as well as validation according to Ramachandran plot and calculation of RMSD (root-mean-square deviation) by using the Proteins program and Protein Structure Alignment panel, respectively.