diff --git a/_posts/2023-10-27-Peptide-Docking-with-ADCP.md b/_posts/2023-10-27-Peptide-Docking-with-ADCP.md index b4c4218a39..af290c2ed9 100644 --- a/_posts/2023-10-27-Peptide-Docking-with-ADCP.md +++ b/_posts/2023-10-27-Peptide-Docking-with-ADCP.md @@ -351,3 +351,70 @@ Performing local search ... done. From the above outputs, we should see that Vina's [optimize](https://autodock-vina.readthedocs.io/en/latest/vina.html#vina.vina.Vina.optimize) function has improved `lig_inter` energy from `-9.087` to `-12.703`, indicating increased protein-peptide interactions after optimization. The `lig_intra` energy has also been improved from `14.634` to `-2.916`, suggesting more stable conformation of the peptide ligand. +Below is an overlay picture of the top-ranked pose, before (cyan) vs. after (magenta) the local optimization: + +![opt-before-after](/assets/img/opt-before-after.jpg) + +It can be seen from the overlay that, the major improvement is the spacing of atoms in peptide residues I and F that were too close in the original ADCP output. + +And an overlay picture of the top-ranked pose (magenta) and the position of sequence `FFEIF` in the crystal structure (cyan): + +![2xpp-adcp-overlay](/assets/img/2xpp-adcp-overlay.jpg) + +It can be seen from the overlay that, residue I is docked at almost the native position. The last (5th) residue F is docked at a near native position, but in a different orientation, probably due to the absence of the subsequent residues. Residue E is docked to interact with a positively charged residue K in the protein receptor. In crystal structure 2XPP, the native orientation of E does not have an apparent interaction with a receptor residue. + +### Compare with Docking in Vina + +With the protein receptor PDBQT file `complex_1H_rec.pdbqt` and the peptide ligand PDBQT file `complex_1H_pep.pdbqt`, it is also possible to perform docking with Vina in Python - + +```python +from vina import Vina + +v = Vina(sf_name='vina') + +v.set_receptor('complex_1H_rec.pdbqt') + +v.set_ligand_from_file('complex_1H_pep.pdbqt') +v.compute_vina_maps(center=[20.076, 10.981, 27.791], box_size=[30, 30, 30]) + +v.dock(exhaustiveness=32, n_poses=20) +v.write_poses('2xpp_ligand_vina_out.pdbqt', n_poses=5, overwrite=True) +``` + +*Output* + +```s +mode | affinity | dist from best mode + | (kcal/mol) | rmsd l.b.| rmsd u.b. +-----+------------+----------+---------- + 1 -6.518 0 0 + 2 -6.414 2.764 8.073 + 3 -6.405 2.881 7.948 + 4 -6.354 2.37 5.629 + 5 -6.352 3.707 9.795 + 6 -6.278 2.483 8.303 + 7 -6.267 2.609 7.185 + 8 -6.258 3.226 9.151 + 9 -6.255 2.494 4.451 + 10 -6.19 2.497 9.221 + 11 -6.136 2.464 5.836 + 12 -6.107 2.744 6.391 + 13 -6.077 2.758 6.186 + 14 -6.067 2.589 4.446 + 15 -6.058 2.308 8.259 + 16 -6.038 2.367 8.083 + 17 -6.035 2.718 6.809 + 18 -6.032 2.075 3.957 + 19 -6.008 2.683 5.735 + 20 -5.976 3.327 8.089 +Performing docking (random seed: -1838194651) ... +``` + +After running three replicates, I found that Vina's output mode#2 (purple) is similar to ADCP's top-ranked mode (magenta) we have been working on: + +![adcp-vina2-overlay](/assets/img/opt-adcp-vina2-overlay.jpg) + +While Vina's output mode#1 (purple) adopts a very interesting conformation, with three F residues stack on top of each other: + +![adcp-vina1-overlay](/assets/img/opt-adcp-vina-overlay.jpg) + diff --git a/assets/img/2xpp-adcp-overlay.jpg b/assets/img/2xpp-adcp-overlay.jpg new file mode 100644 index 0000000000..a2961ad4c0 Binary files /dev/null and b/assets/img/2xpp-adcp-overlay.jpg differ diff --git a/assets/img/adcp-vina-overlay.png b/assets/img/adcp-vina-overlay.png new file mode 100644 index 0000000000..bcc783ff2f Binary files /dev/null and b/assets/img/adcp-vina-overlay.png differ diff --git a/assets/img/adcp-vina2-overlay.jpg b/assets/img/adcp-vina2-overlay.jpg new file mode 100644 index 0000000000..66cf61634a Binary files /dev/null and b/assets/img/adcp-vina2-overlay.jpg differ diff --git a/assets/img/opt-before-after.jpg b/assets/img/opt-before-after.jpg new file mode 100644 index 0000000000..ea65227cfa Binary files /dev/null and b/assets/img/opt-before-after.jpg differ