When we use software such as autodock and chimera, the scores are around -7, -10, -12 kj. The Moldock scores are very high numerically around -100, -150. My question is; Can a conversion be made between these two units? My other question is, the lower the energy score, the further away from zero, does it indicate a more effective bonding? For example, -12 is a much better binding than -7. My last question is: We can see RMSD values when docking operation using Molegro virtual docking software, right?
The docking scores obtained with different scoring functions are not quantitatively comparable. What can be said, however, is that the more negative the docking score, the stronger the binding -- that is the convention; but a positive score does not necessarily mean no binding. RMSD of a query docking pose to the reference binding mode can be calculated in any molecular graphics program, or with a script which compares the corresponding query and reference xyz coordinates.
I am very grateful for your quick reply, thank you very much. I will probably continue to learn with the chimera software. My problem for now is this: I'm doing docking with chimera. And I go to this site https://projects.biotec.tu-dresden.de/plip-web/plip/result/eb3ea754-814b-4e94-b4d0-72b375bfa54c to find out the link types. The site asks us to upload files as pdb. For example, I choose the one whose conformation energy is the best. I save it as PDB, but I get the result that there is no interaction. Normally when I say find hydrogen bonds in the chimera software, it finds a bond, why can't I get normal results on this site? Do you think I'm making a mistake while saving my dock result with chimera?
I recorded in so many different ways. I am sending some of these as attachments, thank you very much for your interest professor
Turgut şekerler, the PDB files contain only the ligand, no protein . . .
thank you so much; When you open it with chimera, the protein and ligand appear, but you say they are not in the output files. I understood the error, thank you very much, I'll try again.
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