Scaffold Placement

The Scaffold Placement module is used to determine the optimal position of a user-defined molecular core within a selected binding site.

Selection of Fragments

The module provides three ways to define the target scaffold:

1. Create a Scaffold - SMILES Input: Manually enter the SMILES notation for the desired scaffold.

Sketch Tool: Click the "Draw" button to manually sketch the scaffold structure. After drawing, press “Confirm” to proceed.

If the uploaded scaffold is already positioned in the selected pocket, you can enable “Use input coordinates” mode.
- This ensures the scaffold remains in its original position, and the system calculates a probability score for that conformation.
To preserve only the internal geometry of the uploaded ligand, enable “Freeze inner geometry” mode.
- This allows docking only for the specified conformation.
If neither option is selected, the scaffold will undergo docking of flexible ligand, generating multiple conformations within the binding site.

The positioning of the scaffold is determined by basic and advanced parameters.

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.

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

False: The formal charges on atoms are preserved as they were initially assigned.
True: Charges and hydrogen atoms are recalculated according to predefined charge assignment rules.

Charge Assignment Rules:

Nitro (-NO₂): Positive charge on nitrogen, negative charge on oxygen.
Carboxyl (-COO⁻): Negative charge on oxygen.
Quaternary Nitrogen: Always carries a +1 charge.
Guanidine (-C(NH₂)₂): The double-bonded nitrogen carries a positive charge.
Uncharged Nitrogen: If no quaternary nitrogens detected, the system will assign a positive charge to one of nitrogen atoms without sp2-hybridized neighbors if such nitrogen atoms are found in the scaffold structure.

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

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.

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).

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.

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.

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.

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.

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”.