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Perform small molecule drug design mutations via the BCL FragmentMutateInterface

References and author information for the BCLFragmentMutateMover mover:

BCLFragmentMutateMover Mover's author(s): Benjamin P. Brown, Vanderbilt University [benjamin.p.brown17@gmail.com] Jeffrey Mendenhall, Vanderbilt University [jeffreymendenhall@gmail.com] Jens Meiler, Vanderbilt University [jens@meilerlab.org]

<BCLFragmentMutateMover name="(&string;)" ligand_chain="(X &string;)"
        conformation_comparer="(SymmetryRMSD &string;)"
        conformer_tolerance="(0.25 &real;)"
        n_max_confs="(100 &non_negative_integer;)"
        n_max_conf_iterations="(500 &non_negative_integer;)"
        sample_chirality="(false &bool;)"
        conf_random_dihed_mutate_prob="(0.0 &real;)"
        conf_generate_3d="(false &bool;)" conf_clash_tolerance="(0.1 &real;)"
        conf_cluster="(true &bool;)" conf_clash_resolution="(0.1 &real;)"
        conf_sample_dihed="(true &bool;)" conf_sample_rings="(true &bool;)"
        conf_sample_bond_angles="(true &bool;)" object_data_label="(&string;)"
        n_max_mutate_attempts="(10 &non_negative_integer;)" />
  • ligand_chain: The chain ID of the ligand residue to be mutated. The specified chain may not contain more than one residue/molecule.
  • conformation_comparer: method with which to compare conformers
  • conformer_tolerance: The amount of tolerance distinguishing conformers
  • n_max_confs: The maximum number of rconformers to generate
  • n_max_conf_iterations: The maximum number of conformer generation iterations to perform; usually 4-5x the maximum number of desired conformers is sufficient
  • sample_chirality: If true, also sample R/S configurations; if false, chirality will not be changed by BCL::Conf
  • conf_random_dihed_mutate_prob: The probability of performing a random dihedral perturbation (ignoring the statistical potential) when generating conformers; generally not recommended outside of benchmarking
  • conf_generate_3d: If true, ignore all input coordinate information when generating conformers; if false, retain input coordinate information to initiate sampling; note that BCL::Conf may have difficulty performing de novo 3D conformer generation for large macrocycles and complex ring systems
  • conf_clash_tolerance: The maximum average angstroms clash present across all atoms in the molecule. A clash is defined as atoms more than three atoms separated that are closer than the sum of their vdw radii - 0.7 Angstroms
  • conf_cluster: Perform leader-follower clustering when generating small molecule conformers; generally recommended as it improves native conformer recovery
  • conf_clash_resolution: maximum number of tries (times number of dihedral angles plus number of bond angles) to resolve clashes permolecule, before clustering. Larger numbers slow the calculation and make it more likely to find kinetically inaccessible conformational space, but a value of 0 makes it hard to sample conformations of strained molecules, so a value around 0.05-0.5 is usually best
  • conf_sample_dihed: If true, sample across dihedral bins; if false, restrict conformational sampling to current dihedral bins
  • conf_sample_rings: If true, sample rings; if false, restrict conformational sampling to current ring conformer
  • conf_sample_bond_angles: If true, sample bond angles and lengths; if false, restrict conformational sampling to current bond angles and lengths
  • object_data_label: (REQUIRED) The BCL Object Data Label specifying the mutate to use and the options with which that mutate will be constructed. To view all of the options available to a mutate, pass 'help' as the argument to the mutate. For example, if you are making an ExtendWithLinker flavor of this mover, in your XML script Mover definition for BCLFragmentMutateMover, the 'object_data_label' attribute would read 'ExtendWithLinker(help)'.
  • n_max_mutate_attempts: The maximum number of retry attempts that can occur for any single mutate move. Retry attempts are initiated when a mutated fragment fails the internal druglikeness filter or when 3D coordinates cannot be generated for the mutated fragment.