Tools for protein and ligand analysis: Difference between revisions

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*[http://wiki.uoft.bkslab.org/index.php/Plop Plop]: minimize ligand and active site
*[http://wiki.uoft.bkslab.org/index.php/Plop Plop]: minimize ligand and receptor.
*[http://wiki.uoft.bkslab.org/index.php/Omega.parm omega.parm]: change settings for ligand conformation generation
*[http://wiki.uoft.bkslab.org/index.php/Omega.parm omega.parm]: change settings for ligand conformation generation in Omega
*[http://wiki.uoft.bkslab.org/index.php/screen3d screen3d]: align ligands in 3D
*[http://wiki.uoft.bkslab.org/index.php/screen3d screen3d]: align ligands in 3D. Useful to see if bioactive conformation is sampled.
*[http://wiki.uoft.bkslab.org/index.php/Phenix Phenix]: calculate electron densities and display them in Pymol
*[http://wiki.uoft.bkslab.org/index.php/Phenix Phenix]: calculate electron densities and display them in Pymol
*[http://wiki.uoft.bkslab.org/index.php/filter.py: filter.py]: calculate atoms distances of DOCK poses
*[http://wiki.uoft.bkslab.org/index.php/filter.py: filter.py]: calculate atoms distances of DOCK poses

Revision as of 19:23, 8 May 2013

  • Plop: minimize ligand and receptor.
  • omega.parm: change settings for ligand conformation generation in Omega
  • screen3d: align ligands in 3D. Useful to see if bioactive conformation is sampled.
  • Phenix: calculate electron densities and display them in Pymol
  • filter.py: calculate atoms distances of DOCK poses
  • FlexPepDock: peptide docking
  • DOCK Sampling: pose sampling in DOCK
  • DOCK6 RMSD: calculate ligand RMSDs