InterfaceScoreCalculator

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InterfaceScoreCalculator

Autogenerated Tag Syntax Documentation:

InterfaceScoreCalculator calculates a myriad of ligand specific scores and appends them to the output file. After scoring the complex the ligand is moved 1000 Å away from the protein. The model is then scored again. An interface score is calculated for each score term by subtracting separated energy from complex energy.

References and author information for the InterfaceScoreCalculator mover:

InterfaceScoreCalculator Mover's citation(s): Lemmon G, and Meiler J. (2012). Rosetta Ligand docking with flexible XML protocols. Methods Mol Biol 819:143-55. doi: 10.1007/978-1-61779-465-0_10.

<InterfaceScoreCalculator name="(&string;)" chains="(&string;)"
        scorefxn="(&string;)" native="(&string;)"
        native_ensemble_best="(false &bool;)" normalize="(&string;)"
        compute_grid_scores="(false &bool;)" score_in_membrane="(false &bool;)"
        grid_set="(default &string;)" />

chains: (REQUIRED) Comma separated chains to dock.
scorefxn: (REQUIRED) Scorefxn of choice.
native: This is your native pdb without interface mutations. If a native structure is specified, 4 additional score terms are calculated: ligand_centroid_travel, ligand_radious_of_gyration, ligand_rms_no_super, and ligand_rms_with_super.
native_ensemble_best: If true, the native pose has multiple residues for the given chains, and the travel and rmsd metrics will be computed as the best (lowest) value from any of them.
normalize: The normalization function you wish to use.
compute_grid_scores: If compute_grid_scores is true, the scores for each grid will be calculated. This may result in the regeneration of the scoring grids, which can be slow.
score_in_membrane: If true, the interface score of the pose will be computed in solution and in the membrane. Requires pose to have membrane_info object as set in RosettaMP.
grid_set: The Grid Set to use when computing grid scores.

The major terms calculated by this mover are the interface terms. The overall interface value is the interface_delta_X term, where X is replaced by the chain of the ligand being used, as specified by the chains option. Other score terms calculated are the component-wise scores in the if_X_scoreterm terms, where X is the chain letter, and the scoreterm is each active scoreterm in the associated scorefunction. Additionally, the ligand_is_touching_X is a crude metric of if the ligand is in contact with the protein.

If the "native" is specified, either in tag or with the -in:file:native option, the following additional terms are calculated:

ligand_centroid_travel. The distance between the native ligand and the ligand in our docked model.
ligand_radius_of_gyration. An outstretched conformation would have a high radius of gyration. Ligands tend to bind in outstretched conformations.
ligand_rms_no_super. RMSD between the native ligand and the docked ligand.
ligand_rms_with_super. RMSD between the native ligand and the docked ligand after rigid-body aligning the two in XYZ space. This is useful for evaluating how much internal ligand flexibility was sampled.

RMSD calculations use an "automorphic" rmsd, which accounts for internal symmetries and equivalent atoms in the ligand (e.g. 180 degree phenyl ring flips).

For the ligand_centroid_travel and ligand_rms_no_super terms, it is assumed that the native has already been aligned with the input protein -- the ligand coordinates are used as-is, and no protein/protein alignment is done prior to the travel and rmsd calculation.

If the native_ensemble_best option is enabled, it is assumed the working pose has only a single residue on the relevant chain, and the "native" pose has one or more residues on the corresponding chain. The travel and rmsd values will be calculated separately for each of the residues in the corresponding chain, and the lowest value will be reported. This can be useful if there are multiple native states which can all be considered "correct".

InterfaceScoreCalculator

InterfaceScoreCalculator

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