Tools for protein and ligand analysis: Difference between revisions
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*[http://wiki.uoft.bkslab.org/index.php/screen3d screen3d]: Align ligands in 3D. Useful to see if bioactive ligand conformation is sampled. | *[http://wiki.uoft.bkslab.org/index.php/screen3d screen3d]: 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/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 atoms distances of DOCK poses. Useful to analyze docking results. | *[http://wiki.uoft.bkslab.org/index.php/filter.py: filter.py]: How to calculate atoms 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/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/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. | *[http://wiki.uoft.bkslab.org/index.php/Calculate_DOCK6_RMSD DOCK6 RMSD]: Easy tool calculate ligand RMSDs using DOCK 6.6. | ||
Revision as of 19:32, 8 May 2013
- 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: 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 atoms 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.