Tools for protein and ligand analysis: Difference between revisions
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*Plop | *[http://wiki.uoft.bkslab.org/index.php/Plop Plop]: minimize ligand and active site | ||
*omega.py | *[http://wiki.uoft.bkslab.org/index.php/omega.py omega.py]: change settings for ligand conformation generation | ||
*screen3d | *[http://wiki.uoft.bkslab.org/index.php/screen3d screen3d]: align ligands in 3D | ||
*Phenix | *[http://wiki.uoft.bkslab.org/index.php/Phenix Phenix]: calculate electron densities and display them in Pymol | ||
*filter.py | *[http://wiki.uoft.bkslab.org/index.php/filter.py: filter.py]: calculate atoms distances of DOCK poses | ||
*FlexPepDock | *[http://wiki.uoft.bkslab.org/index.php/FlexPepDock FlexPepDock]: peptide docking | ||
*[http://wiki.uoft.bkslab.org/index.php/Calculate_DOCK6_RMSD | *[http://wiki.uoft.bkslab.org/index.php/Dock_Ligand_Clustering Niu Huang DOCK]: ligand clustering and pose sampling | ||
*[http://wiki.uoft.bkslab.org/index.php/Calculate_DOCK6_RMSD DOCK6 RMSD]: calculate ligand RMSDs | |||
Revision as of 23:45, 18 April 2013
- Plop: minimize ligand and active site
- omega.py: 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