View source for Tools for protein and ligand analysis

*[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]: How to change settings for ligand conformation generation in Omega.
*[http://wiki.uoft.bkslab.org/index.php/screen3d screen3d]: How to align ligands in 3D. Useful to see if bioactive ligand conformation is sampled.
*[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]: How to calculate atom distances of DOCK poses to reference coordinates. Useful to analyze docking results.
*[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]: How to check if you actually sampled a bioactive orientation in DOCK (using Niu Huang's ligand clustering DOCK binary).
*[http://wiki.uoft.bkslab.org/index.php/Calculate_DOCK6_RMSD DOCK6 RMSD]: Easy tool calculate ligand RMSDs using DOCK 6.6.


[[Category:Software]]
[[Category:Tutorials]]