I have tried to do a blind docking through Achilles online software as a first approach because I don't know the binding site of my receptor. The problem is that my ligand seems to have more than 12 torsional degrees of freedom and the software asks for less. I have tried to minimize them through Autodock Tools setting them to 12 (the limit for the software) and saved the file as pdbqt but when I upload it, it gives me the same error message again. I think I am doing something wrong. Is there a way to minimize the torsional degrees of freedom of my ligand and then upload the file? Does someone have a suggestion of how can I do blind docking else-wise? Forgive me but I am very new at this.
An alternative to a purely blind docking is an approach that starts with identifying pockets/cavities/clefts in the target protein, and follows with docking to those pockets/cavities/clefts large enough, and with physico-chemical properties suitable, for the binding of the ligands in question.
https://proteins.plus/
Martin Klvana thank you for your help! The thing is that I have the crystal structure of my protein and I predicted the structure of the peptide I want to test if acts as ligand to this protein. So it is not an "official" or known ligand for this specific protein. That's why I want to do a blind Docking. To check if and where it interacts with this receptor. Either way I am very grateful for your proposal! It seems to be a useful tool!
- Badges
- Science topic
- Similar topics
- Filing