Tools for protein and ligand analysis: Difference between revisions
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*[http://wiki.uoft.bkslab.org/index.php/Plop Plop]: minimize | *[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 | *[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 | *[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]: 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 | *[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]: 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]: | *[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]: calculate ligand RMSDs | *[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]] | |||
Latest revision as of 19:59, 17 March 2014
- 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: How to 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 atom distances of DOCK poses to reference coordinates. 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 (using Niu Huang's ligand clustering DOCK binary).
- DOCK6 RMSD: Easy tool calculate ligand RMSDs using DOCK 6.6.