1. Gambar 2d di chembio draw (save as .

cdx)
2. Gambar 3d
3. Optimasi/minimisasi dengan games interface (MM2 minimize) -> catat calculation
Semakin kecil e minimisasi, semakin stabil -> save as xx_optimize.mol2

Install spdb viewer untuk visualisasi file pdb

1. Control panel (select rantai A, invert selection, build remove select residue)
2. Delete ligand (build, remove selected…)
3. Save current layer (filetype .pdb)

Autodock (memperbaiki struktur)

1. Open cox2.pdb
2. Edit (delete water (simulasi docking dalam vakum), hydrogens (merge non-polar), hydrogen add
(polar only), charge (untuk bias docking biar ada interaksi) -> protein : add Kollman charge) Save
grid, macromolecule, choose, cox2, select molecule, save cox2.pdbqt)
3. Buka baru autodock
4. Ligand andro_optimized.mol2 (edit charges compute gesteiger (0.0 tidak ada yg bias di
tambahkan)
5. Lihat torsi (ligand, choose, ligand torsion tree chose torsion, done) -> save ligand, save as .pdbqt

PyRx

1. Bikin folder kerja (edit, preferences, workspace, browse, CPU ganti) tutup PyRx, buka lagi
2. Vina Wizard, start, add ligand, andro.pdbqt, add macromolecule, cox2.pdbqt, select2), forward
3. Cari situs aktif
(kalo ga tau binding site, pake metode blind docking -> kotaknya maximize)
(kalo tau, kotaknya dikecil2 disebesar koordinat)
Run Vina
4. Konformasi pertama = delta G
5. Analisis ikatan buka autodock tools (open autodock vina result, macromolecule, andro
optimized_out)
6. Anlyze macromolecule open macromolecules,
7. Analyze, docking, show interaction, checklist hydrogen bonds
8. Bandingin dengan jurnalnya, interaksinya di asam amino yg mana