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 receptor.  
*[http://wiki.uoft.bkslab.org/index.php/Plop Plop]: Introduction to this powerful tool to minimize ligands and receptors/active sites.  
*[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/Omega.parm omega.parm]: How to change settings for ligand conformation generation in Omega.
*[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/screen3d screen3d]: Align ligands in 3D. Useful to see if bioactive ligand 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]: How to 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]: How to calculate atoms distances of DOCK poses. Useful to analyze docking results.
*[http://wiki.uoft.bkslab.org/index.php/FlexPepDock FlexPepDock]: peptide docking
*[http://wiki.uoft.bkslab.org/index.php/FlexPepDock FlexPepDock]: Flexible peptide docking using Rosetta.
*[http://wiki.uoft.bkslab.org/index.php/Dock_Sampling DOCK Sampling]: pose sampling in DOCK
*[http://wiki.uoft.bkslab.org/index.php/Dock_Sampling DOCK Sampling]: How to check if you actually sampled a bioactive orientation in DOCK. Sampling is done using Niu Huang's ligand clustering DOCK binary.
*[http://wiki.uoft.bkslab.org/index.php/Calculate_DOCK6_RMSD DOCK6 RMSD]: calculate ligand RMSDs
*[http://wiki.uoft.bkslab.org/index.php/Calculate_DOCK6_RMSD DOCK6 RMSD]: Easy tool calculate ligand RMSDs using DOCK 6.6.

Revision as of 19:30, 8 May 2013

  • Plop: Introduction to this powerful tool to minimize ligands and receptors/active sites.
  • omega.parm: How to change settings for ligand conformation generation in Omega.
  • screen3d: Align ligands in 3D. Useful to see if bioactive ligand conformation is sampled.
  • Phenix: How to calculate electron densities and display them in Pymol.
  • filter.py: How to calculate atoms distances of DOCK poses. Useful to analyze docking results.
  • FlexPepDock: Flexible peptide docking using Rosetta.
  • DOCK Sampling: How to check if you actually sampled a bioactive orientation in DOCK. Sampling is done using Niu Huang's ligand clustering DOCK binary.
  • DOCK6 RMSD: Easy tool calculate ligand RMSDs using DOCK 6.6.