Tools for protein and ligand analysis

• 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.