Ususally, users come to Rosetta with an idea of the biological problem they want to solve. Sometimes, users come with an input structure and the notion that they want to perform a particular type of sampling, whether via running an application or using a RosettaScripts mover. Here, we have categorized Rosetta's RosettaScripts-enabled movers by the type of structural perturbation they perform, but the biological problems page will better serve you for application use. If neither page helps, perhaps you haven't determined what the problem is?

Structure determination via fragment substitution

  • AbscriptLoopCloserCM
    handles loop closure in ab initio relax circumstances
  • AbscriptMover

Structure generation

Residue Insertion and Deletion

Structure optimization

  • IdealizeMover
    Replace every residue with a version with bond lengths and angles from the database. Add constraints to maintain original hydrogen bonds. Then, minimize every side-chain and backbone dihedral (except proline phi) using dfpmin.
  • FinalMinimizer
  • SaneMinMover
  • TaskAwareMinMover
  • Symmetrizer
    Functionally an optimization mover; will take a pose with sufficiently small deviations from symmetry and resolve them.
  • TaskAwareSymMinMover
    SymMinMover
    minimize with symmetry
  • LocalRelax
    FastRelax
    Repeatedly repack sidechains and minimize sidechains and backbone while ramping the repulsive weight up and down. Respects resfiles, movemaps, and task operations.
  • RepackMinimize Like a single cycle of relax, with a constant repulsive weight.
  • MinPackMover
  • EnzRepackMinimize
  • MinMover
  • MinimizationRefiner
  • NormalModeMinimizer

Ensemble generation

Backbone degrees of freedom

  • Backrub
    BackrubDD
    BackrubSidechain
    ShortBackrubMover
    A particular form of backbone movement intended to coordinate with maintaining particular side chain positions.
  • Small Make small perturbations to a backbone degree of freedom
  • Shear Make small perturbations to one dihedral of a residue and contravarying perturbations to the other dihedral, to avoid a "lever arm effect"
  • SetTorsion
    Either set a torsion to a value or perturb a torsion by a value (with the perturb flag)
  • MinimizeBackbone
    Just minimize the backbone
  • RandomOmegaFlipMover Flip a random omega angle; most useful for peptoids
  • BackboneTorsionPerturbation
  • BackboneTorsionSampler
  • BBGaussian

Sidechain degrees of freedom

Any conformational degree of freedom

  • RandomTorsionMover
    Perturbs a random torsion selected from a movemap

Loop conformational sampling

  • AnchoredGraftMover
    a composite mover that does a lot of loop modeling followed by repacking to graft in residues
  • KicMover
  • LegacyKicSampler
  • SmallMinCCDTrial
  • ShearMinCCDTrial
  • LoopBuilder
  • LoopCM
  • LoopCreationMover
  • LoopFinder
  • LoopHash
    LoopHashDiversifier
    LoopHashLoopClosureMover
    The LoopHash algorithms constitute a very rapid way to draw on loop conformations from fragment libraries that could achieve a given closure
  • LoopLengthChange
  • LoopModeler
  • LoopMoverFromCommandLine
  • LoopMover_Perturb_CCD
  • LoopMover_Perturb_KIC
  • LoopMover_Perturb_QuickCCD
  • LoopMover_Perturb_QuickCCD_Moves
  • LoopMover_Refine_Backrub
  • LoopMover_Refine_CCD
  • LoopMover_Refine_KIC
  • LoopMover_SlidingWindow
  • LoopProtocol
  • LoopRefineInnerCycleContainer
  • LoopRelaxMover
  • LoopRemodel
  • LoophashLoopInserter
  • LoopmodelWrapper
  • CCDEndsGraftMover
  • CCDLoopCloser
  • CCDLoopClosureMover
  • DefineMovableLoops
  • GeneralizedKIC
    An enormous, intricate system that largely operates on its own to perform kinematic loop closure on an arbitrary sequence of atoms.

Docking

  • DARC app
    Via a ray casting algorithm particularly fast on GPUs
  • FlexPepDock
    Concurrently samples backbone degrees of freedom on the peptide
  • SymDockProtocol
    Symmetric oligomer docking
  • RigidBodyTransMover
    manually manipulate the relative position of two bodies across a jump
  • RigidBodyPerturbNoCenter
  • UnbiasedRigidBodyPerturbNoCenter
  • UniformRigidBodyCM
  • Docking
  • DockingInitialPerturbation
  • DockingProtocol
  • DnaInterfaceMinMover
  • SymFoldandDockRbTrialMover
  • HighResDocker
  • DockSetupMover
  • DockWithHotspotMover

Chemical connectivity

  • ForceDisulfides
    Given a list of residue pairs (for example, disulfides), repack residue shells around them but do not change the CYS-type residues themselves.
  • DisulfideInsertion
    Mutates two residue positions to CYS:disulfide, link them conformationally, and add constraints to have good disulfide distance, angle, and dihedral to the pose. Intended for adding a disulfide to short potentially macrocyclic peptides.
  • DisulfideMover
    Given two residue positions, mutate both to CYS:disulfide and link them conformationally; do no repacking or minimization
  • Disulfidize
    Tries every possible pair of residues in a pose to try to introduce one or more new disulfides as long as they score well

Design

Analysis

Symmetric interfaces

Molecular dynamics codes

Peptidomimetics

  • NcbbDockDesign
  • OopCreatorMover
  • OopDockDesign

Antibody Modeling and Design

See Also