Tools for protein and ligand analysis

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  • 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.
  • 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.