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 | *[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