1 To begin, 2 open the traditional Chinese Medicine Systems 3 Pharmacology database. 4 Using the chemical name search box, 5 search the selected ingredient names 6 to download the corresponding 3D structure files 7 in Mol2 format. 8 To download the crystal structures of the key targets, 9 open the RCSB Protein database.
10 In the search box, 11 search the target names 12 and download the corresponding 13 crystal structure files in PDB format. 14 Import ingredients and target structure files 15 in the analysis software. 16 Click Edit, then Delete Water to delete water molecules.
17 To add hydrogens, click on Edit, Hydrogens, and Add. 18 Set the ingredients as the ligand. 19 Select whole targets as the receptor 20 and perform blind docking.
21 To determine the range of molecular docking, 22 select the receptor and ligand in sequence. 23 Click on Grid, then Grid Box to adjust the grid box 24 to include the entire model. 25 Click on File and Close to save the current grid box status 26 and save the files in GPF format.
27 Now click on Run and Run Auto Grid Four, 28 click Parameter File Name, and Browse, 29 to select the GFP file. 30 Then click the Launch button. 31 For molecular docking, 32 open the auto doc four and click on docking, Macromolecule, 33 and set rigid file name to select the receptor.
34 Then click on Docking, Ligand and open, 35 or choose to select the ligand. 36 Now click on Docking 37 and Search Parameters to set operation algorithms. 38 Then click Docking and Docking Parameters 39 to set docking parameters.
40 Select the DPF file and click the launch button. 41 Save files in the DPF format. 42 Click on Analyze, Docking, 43 and open to select the DLG file.
44 Then click on Analyze and Macromolecule 45 to open the receptor. 46 Now click on Analyze, Confirmations, and Play, 47 ranked by energy to analyze the results. 48 Finally, click Set Play, 49 and write complex to save the results in PDBQT format.
50 Import the docking files into PyMOLE, 51 then select the ligand and click on Action, Find, 52 Polar Contracts and to other atoms and object 53 to display hydrogen bonds between ligands 54 and the external environment. 55 Click on single letter C to change color. 56 Click Action and Extract Object.
57 Click Show, then Sticks, 58 to show the stick structure of the receptor, 59 identify the residuals connected to ligands 60 and show the stick structure. 61 Then click Wizard and Measurement 62 and click on two atoms in sequence. 63 Click Label then Residue to show the label of the residues.
64 If necessary, adjust the background color and transparency. 65 Finally, click File, then Export Image As 66 to save the picture. 67 In the atopic dermatitis group, 68 GEO database analysis revealed upregulation 69 of P-P-A-R-G, E-G-F-R, T-N-F 70 and P-T-P-R-C MMP Nine, MAPK 14, 71 and CASP Three were downregulated.
72 Docking analysis confirmed the interaction 73 between active SDG components 74 and potential target proteins 75 indicating their significant role in anal eczema treatment. 76 Indigo and Berberrubine demonstrated strong binding activity 77 with energy's less than minus five kilo calories per MOL, 78 emphasizing their therapeutic potential.
