Skip to main content

Site Map

The Site Map module is designed for placing triatomic fragments (probes) in a specified binding pocket of a protein. This process helps identify potential hydrogen bonding interactions, which play a crucial role in non-covalent binding between ligands and proteins.

Selection of Fragments​

29 triatomic fragments are available for selection.

flow 0
flow 1
  • You can choose one or multiple fragments from the list.
  • Solid lines represent actual atomic connections within a triatomic probe.
  • Dashed lines indicate potential variations of the selected fragment, providing alternative structures.

Should be noted that time of execution strongly depends on the number of selected probes.

Setting Parameters​

The placement of probes is influenced by multiple basic and advanced parameters.

Basic Parameters​

  1. Check H-bonds (True/False)
    • False: Probes are placed without checking for hydrogen bonding interactions.
    • True: Only probes forming at least one hydrogen bond with the protein will be retained.
flow 4

Hydrogen bonds are evaluated based on the distance between heavy atoms: ligand acceptor atoms and protein donor atoms (and vice versa).

  1. Maximum Number of Conformations (1–10 or “All”)
    • Determines the maximum number of probe positions generated in the pocket.
    • Selecting “All” retains every generated conformation.

Advanced Parameters​

Note: Advanced parameters should be modified only by experienced users.


  1. Maximum H-bond Distance (Å) (3.0–4.0, Default: 3.8 Å) -Defines the maximum distance for an interaction to be considered a hydrogen bond. -Can only be set if Check H-bonds is True.

  1. Vina score (-10 to 5, Default: 0) -Represents the binding energy between the probe and the protein. -Calculated using AutoDock Vina (Trott O., Olson AJ., AutoDock Vina: Improving the Speed and Accuracy of Docking).

  1. Maximum Clashes Number (0–10, Default: 5) -Limits steric clashes between the probe and protein atoms. -Clashes are identified using a predefined dictionary of minimum allowed distances in non-covalent interactions.

  1. Final Confidence Score (-12–0, Default: -3.5) -Determines the likelihood of a probe's correct positioning. -A more negative score indicates lower reliability for that probe's placement. - Only poses with scores lower than the specified threshold are retained.

  1. Minimization Shift (Å) (1.0–5.0, Default: 2.0 Å)
    • Defines the maximum allowed movement of the probe after energy minimization.
    • Used to refine probe placement and improve accuracy.

  1. Pocket Mismatch Limit (Å) (0.5–2.5, Default: 1.3 Å)
    • Defines the maximum allowed movement of the probe after energy minimization.
    • Used to refine probe placement and improve accuracy.

Parameter Customization​

  • Each parameter has a default value designed for general use.
  • If stricter criteria are needed, tighten the settings (e.g., reducing pocket mismatch limits).
  • If no probes are found, relax the constraints (e.g., increasing the clash limit).
  • To restore defaults, press “Default Parameters”.
  • To apply changes, press “Confirm”.