PacVIEW Documentation

Receptor-Ligand Interactions and Docking Results visualisation

PacVIEW enables graphic visualisation to study and interpret docking results.
It offers two visualisation modes: Receptor-Ligand Interactions and Docking Results.
Inputs
PacVIEW requires two different files for each mode:
For Receptor-Ligand Interactions mode:
  1. a file containing the Receptor structure
  2. a file containing the Ligand structure
For Docking Results mode:
  1. a file containing the Reference structure
  2. a file containing the Docked structure(s)
The user can submit these files in different chemical file formats: PDB, PDBQT, SDF, MOL2, MOL, ENT, CIF, GZ.
Maximum file size: 50 MB.
Visualisation modes
PacVIEW can execute 2 different types of molecular visualisation:
  • Receptor-Ligand Interactions: displays the ligand into the binding pocket of its receptor, and allows the visualisation of the key receptor-ligand interactions.
    The user can choose the types of interactions to be investigated: Hydrogen Bond, Ionic Interaction, Hydrophobic, Cation-π, π-Stacking, Metal Coordination, Halogen Bond, Backbone HB, Water HB, Weak HB.
  • Docking results: displays the docked pose(s) compared with the reference structure.
    The user can select the specific docked pose(s) to display (maximum limit: 10 poses).
    This mode can be useful to visualise the same input files used in ProRMSD.
Output
The output consists in the interactive 3D structures of loaded files.
Each structures can be displayed in multiple style modes and colours selected by the users.
The user can rotate and translate the structure and choose different visualisation parameters.
User can save images of the visualised molecules and interactions at different resolutions:
  • Medium Quality: image factor 6
  • High Quality: image factor 12
Tips for beginners
Using PacVIEW, the calculated numerical value of RMSD between two poses can be associated with a visualisation of spatial differences.
For a more reliabile evaluation of re-docking results, it may be useful to associate the RMSD value with the analysis of receptor-ligand interactions.

PacVIEW

SUBMIT A JOB