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 active site | ||
*[http://wiki.uoft.bkslab.org/index.php/ | *[http://wiki.uoft.bkslab.org/index.php/Omega.parm omega.parm]: change settings for ligand conformation generation | ||
*[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 | ||
*[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 | ||
Revision as of 22:08, 29 April 2013
- Plop: minimize ligand and active site
- omega.parm: change settings for ligand conformation generation
- screen3d: align ligands in 3D
- Phenix: calculate electron densities and display them in Pymol
- filter.py: calculate atoms distances of DOCK poses
- FlexPepDock: peptide docking
- Niu Huang DOCK: ligand clustering and pose sampling
- DOCK6 RMSD: calculate ligand RMSDs