Wandré Nunes de Pinho Veloso

3 Questions 8 Answers 0 Followers

Questions related from Wandré Nunes de Pinho Veloso

Which parameters of Autodock Vina to redocking some molecules?

I am trying to use the Autodock Vina to redocking some structures, but, the results are not so good.There is just one result of docking in the same subpocket, but is very different of the...

04 October 2016 8,423 4 View

When I download a PDB ligand file, there is two types of file: IDEAL and MODEL. Whats the difference?

In RCSB PDB, I can download much ligand files and use it for docking, but, there is two options to download a ligand: Model and Ideal.In RCSB PDB site I don't find what is the difference between...

06 July 2016 9,889 8 View

How can I calculate RMSD to crystalographic ligand and a docked ligand?

I found a function in RDKit (rdMolAlign.AlignMol), but I can't import PDBQT file to RDKit... I docked a ligand with AutoDock Vina and was generated a PDBQT file with the results of docking and I...

23 June 2016 1,469 6 View