Docking strategies

This section does not pretend to be a comprehensive User Guide. It does, however, highlight the key steps the user must take for different docking strategies, and may serve as a useful checklist in writing such a guide in the future.

Standard docking

By standard docking, we refer to docking of a flexible, untethered ligand to a receptor in the absence of explicit structural waters or any experimental restraints.

Standard docking workflow

  1. Prepare a MOL2 file for the protein or nucleic acid target, taking into account the atom typing issues described above for MOL2 file parsing. The recommendation is to prepare an all-atom MOL2 file and allow rDock to remove the non-polar hydrogens on-the-fly.

    Important Make sure that any non-standard atom names and substructure names are defined in $RBT_ROOT/data/sf/RbtIonicAtoms.prm in order for the assignment of distributed formal charges to work correctly. Make sure that the Tripos atom types are set correctly. rDock uses the Tripos types to derive other critical atomic properties such as atomic number and hybridisation state.

    Note The rDock MOL2 parser was developed to read the CCDC/Astex protein.mol2 files, therefore this validation set is the de facto standard reference. You should compare against the format of the CCDC/Astex MOL2 files if you are in doubt as to whether a particular MOL2 file is suitable for rDock.

  2. Prepare a system definition file. At a minimum, you need to define the receptor parameters, the cavity mapping parameters (SECTION MAPPER) and the cavity restraint penalty (SECTION CAVITY). Make sure you define the RECEPTOR_FLEX parameter if you wish to activate sampling of terminal OH and NH3+ groups in the vicinity of the docking site.

  3. Generate the docking site (.as) file using rbcavity. You will require a reference bound ligand structure in the coordinate space of the receptor if you wish to use the reference ligand cavity mapping method.

  4. Prepare the ligand SD files you wish to dock, taking into account the atom typing issues described above for SD file parsing. In particular, make sure that formal charges and formal bond order are defined coherently so that there are no formal valence errors in the file. rDock will report any perceived valence errors but will dock the structures anyway. Note that rDock never samples bond lengths, bond angles, ring conformations, or non-rotatable bonds during docking so initial conformations should be reasonable.

  5. Run a small test calculation to check that the system is defined correctly. For example, run rbdock from the command line with a small ligand SD file, with the score-only protocol (-p score.prm) and with the -T 2 option to generate verbose output. The output will include receptor atom properties, ligand atom properties, flexibility parameters, scoring function parameters and docking protocol parameters.

  6. When satisfied, launch the full-scale calculations. A description of the various means of launching rDock is beyond the scope of this guide.

Tethered scaffold docking

In tethered scaffold docking, the ligand poses are restricted and forced to overlay the substructure coordinates of a reference ligand. The procedure is largely as for standard docking, except that:

  • Ligand SD files must be prepared with the rbtether utility to annotate each record with the matching substructure atom indices, and to transform the coordinates of each ligand so that the matching substructure coordinates are overlaid with the reference substructure coordinates. This requires a Daylight SMARTS toolkit license.

  • The system definition file should contain a SECTION LIGAND to define which of the the ligand degrees of freedom should be tethering to their reference values. Tethering can be applied to position, orientation and dihedral degrees of freedom independently. Note that the tethers are applied directly within the chromosome representation used by the search engine (where they affect the randomisation and mutation operators), and therefore external restraint penalty functions to enforce the tethers are not required.

Important The reference state values for each tethered degree of freedom are defined directly from the initial conformation of each ligand as read from the input SD file, and not from the reference SD file used by rbtether. This is why the ligand coordinates are transformed by rbtether, such that each ligand record can act as its own reference state. The reference SD file used by rbtether is not referred to by the docking calculation itself.

It follows from the above that tethered ligand docking is inappropriate for input ligand SD files that have not already been transformed to the coordinate space of the docking site, either by rbtether or by some other means.

Example ligand definition for tethered scaffold

This definition will tether the position and orientation of the tethered substructure, but will allow free sampling of ligand dihedrals.

SECTION LIGAND
   TRANS_MODE TETHERED
   ROT_MODE TETHERED
   DIHEDRAL_MODE FREE
   MAX_TRANS 1.0
   MAX_ROT 30.0
END_SECTION

Docking with pharmacophore restraints

In pharmacophore restrained docking, ligand poses are biased to fit user-defined pharmacophore points. The bias is introduced through the use of an external penalty restraint, which penalises docking poses that do not match the pharmacophore restraints. Unlike tethered scaffold docking, there is no modification to the chromosome operators themselves, hence the search can be inefficient, particularly for large numbers of restraints and/or for ligands with large numbers of matching features. Pre-screening of ligands is based purely on feature counts, and not on geometric match considerations.

The implementation supports both mandatory and optional pharmacophore restraints. The penalty function is calculated over all mandatory restraints, and over (any NOPT from N) of the optional restraints. For example, you may wish to ensure that any 4 from 7 optional restraints are satisfied in the generated poses.

The procedure is largely as for standard docking, except that:

  • You should prepare separate pharmacophore restraint files for the mandatory and optional restraints. Note that optional restraints do not have to be defined, it is sufficient to only define at least one mandatory restraint.

  • The system definition file should contain a SECTION PHARMA to add the pharmacophore restraint penalty to the scoring function.

Docking with explicit waters

Explicit structural waters can be loaded from an external PDB file, independently from the main receptor model, by adding a SECTION SOLVENT to the system definition file. The user has fine control over the flexibility of each water molecule. A total of 9 flexibility modes are possible, in which the translational and rotational degrees of freedom of each water can be set independently to FIXED, TETHERED, or FREE. Thus, for example, it is possible to define a water with a fixed oxygen coordinate (presumably at a crystallographically observed position), but freely rotating such that the orientation of the water hydrogens can be optimised by the search engine (and can be ligand-dependent).

Note In the current implementation, solvent refers strictly to water molecules, and the format of the water PDB file is very strictly defined. In future implementations it is anticipated that other, larger (and possibly flexible) molecules will be loadable as solvent, and that other file formats will be supported.

Explicit waters workflow

  1. Prepare a separate PDB file for the explicit waters according to the format prescribed (the section called Water PDB file format).

  2. Add a SECTION SOLVENT to the system definition file and define the relevant flexibility parameters (Table 13). The minimal requirement is to define the FILE parameter.

  3. Decide whether you wish to have different per-solvent flexibility modes (defined via the occupancy values and temperature factor values in the PDB file (Table 17)), or whether you wish to have a single flexibility mode applied to all waters (defined via the TRANS_MODE and ROT_MODE values in the SECTION SOLVENT of the receptor .prm file).

    Important If you wish to use per-solvent flexibility modes (that is, you wish to set different modes for different waters) make sure that you do not define TRANS_MODE or ROT_MODE entries in the SECTION SOLVENT as these values will override the per-solvent values derived from the temperature factors in the PDB file.

  4. If you have defined any waters with TETHERED translational or rotational degrees of freedom, define MAX_TRANS and/or MAX_ROT values as appropriate (or accept the default values). The tethered ranges are applied to all tethered waters and can not be defined on a per-solvent basis at present.