I am trying to do molecular docking studies for metal complexes using crystal structure of oligonucleotide from PDB 2O1I. However, trying to perform it with Swissdock or Molegro failed because they recognize the oligonucleotide as a ligand which can not be used for docking. The paper that used the same PDB 2O1I for molecular docking used ICM-pro software. I am asking if anyone is aware of free alternatives to ICM in this aspect ?
Dear Moustafa Gabr,
Have you try the docking study by using AutoDock 4.2 program package from the Scripps Research Institute?
What about HADDOCK?!, it's highly reliable for this kind of docking, charged ligands into Nucleic acid receptors, but you need to modify your PDB file to be recognizable on the python-based package.
- Badges
- Science topic
- Similar topics
- Engineering
- Modeling