CycpepRigidBodyPermutationMover

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CycpepRigidBodyPermutationMover

Table of Contents

- CycpepRigidBodyPermutationMover
- See Also

Description

The CycpepRigidBodyPermutationMover is used to consider alternative docked conformations of a cyclic peptide bound to a protein. Given a residue selector that selects the cyclic peptide portion, the mover superimposes the cyclic peptide on a cyclic permutation or inverse cyclic permutation of itself, adds a small random offset and orientation permutation, and updates the coordinates of only the cyclic peptide atoms. The mover can act in one of two modes. In "randomized_perturbation" mode, the cyclic permutation is random, and will vary from run to run (nstruct to nstruct). In "set_permutation" mode, the user specifies the permutation offset, and whether or not a reverse permutation should be used. Note that this mover only does rigid body perturbations. It is highly recommended to follow this with side-chain repacking and energy minimization (for example, with the FastRelax mover).

Author and Development History

The mover was written by Vikram K. Mulligan, Center for Computational Biology, Flatiron Institute (vmulligan@flatironinstitute.org) on 9 Dec. 2021. It was tested by Stephan Kudlacek, Menten AI (stephan.kudlacek@menten.ai).

Code Organization

The mover and its creator are found in the protocols::cyclic_peptide namespace, and in the Rosetta/main/source/src/protocols/cyclic_peptide directory.

Usage

Autogenerated Tag Syntax Documentation:

A mover that takes a cyclic peptide and alters its position (rigid-body transform), superimposing it on a cyclic permutation or reverse cyclic permutation of itself. Created 22 November 2021 by Vikram K. Mulligan and Stephan Kudlacek.

References and author information for the CycpepRigidBodyPermutationMover mover:

CycpepRigidBodyPermutationMover Mover's author(s): Vikram K. Mulligan, Systems Biology Group, Center for Computational Biology, Flatiron Institute vmulligan@flatironinstitute.org Stephan Kudlacek, Menten AI stephan.kudlacek@menten.ai

<CycpepRigidBodyPermutationMover name="(&string;)" mode="(&string;)"
        allow_random_inversion="(&bool;)" set_permutation_offset="(&integer;)"
        set_inverse_alignment="(&bool;)" random_position_offset="(&real;)"
        random_orientation_perturbation="(&real;)" residue_selector="(&string;)" />

mode: The mode for this mover, used to set whether we're setting a particular permutation or whether we're drawing randomly from possible permutations. Allowed settings are: set_permutation and randomized_permutation.
allow_random_inversion: If true (the default), then in randomized_permutation mode, allowed permutations include those that align the peptide to a reversed permutation of itself. If false, then only forward permutations are allowed. Only used in randomized_permutation mode. See set_inverse_alignment for the related setting for set_permutation mode.
set_permutation_offset: The cyclic permutation offset. If aligning to the forward sequence, this is the offset in the forward direction along the sequence. If aligning to the reversed sequence, this is the offset in the backward direction. Only used in set_permutation mode.
set_inverse_alignment: Sets whether we align the peptide to its forward sequence or to its reversed sequence. Only used in set_permutation mode. See allow_random_inversion for the related setting for randomized_permutation mode.
random_position_offset: The magnitude of a random offset, in Angstroms, that will be applied to the peptide position after every cyclic permutation. The direction is wholly random. Set this to 0.0 to disable. Used in all modes.
random_orientation_perturbation: The magnitude of a random perturbation, in degrees, that will be applied to the peptide orientation after every cyclic permutation. The rotation axis is wholly random, while the center of rotation is the peptide centroid. Set this to 0.0 to disable. Used in all modes.
residue_selector: An optional residue selector, used to select the cyclic peptide part of a pose. The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3.

CycpepRigidBodyPermutationMover