Rosetta 3.1 Release Manual

Loop Modeling Application

This release of Rosetta includes updates to the Rosetta 3.x cyclic coordinate descent (CCD) and kinematic closure (KIC) loop modeling application. You can find the code for the loop modeling protocols in src/apps/public/loop_modeling/. The executable is located at bin/loopmodel.*. A sample package is in ReleaseSamples/Loop/.

Metadata

This document was last edited August 10th 2009 by Daniel J. Mandell.
The CCD submodes of the application were written by: The kinematic closure (KIC) submodes of the application were written by Kinematic closure is a modeling technique inspired by inverse-kinematics from robotics. The method operates locally on a peptide segment, leaving the endpoints fixed, making it well-suited for loop modeling and interface design. 2N-6 backbone torsion angles (phi/psi) of an N-residue segment are set to values sampled from a residue-specific Ramachandran map, and N-CA-C bond angles are sampled within half a standard deviation of canonical values, effectively opening the chain. The remaining 6 phi/psi torsions are then solved by kinematic closure so that the segment is closed exactly in a new conformation (0 to 16 solutions may be found). For loop modeling, this calculation is iterated in a simulated annealing Metropolis Monte Carlo protocol.

References

For CCD loop modeling (flags containing 'ccd') please cite The CCD algorithm is described in For kinematic loop modeling (flags containing 'kic') please cite Underlying principles of the implemented kinematic closure algorithm are described here

Input Files

  1. Start pdb
  2. Loops file

    Here is the loop file format. The columns are whitespace delimited. Only 1-3 are necessary.

    column1  "LOOP":     Literally the string LOOP, identifying this line as a loop
                         In the future loop specification files may take other data.
    column2  "integer":  Loop start residue number
    column3  "integer":  Loop end residue number
    column4  "integer":  Cut point residue number, >=startRes, <=endRes. Default or 0: let LoopRebuild choose cutpoint randomly.
    column5  "float":    Skip rate. default - never skip
    column6  "boolean":  Extend loop. Default false
    
    For Example: A legal line in a loops file (the line by itself is a legal file):
    LOOP 23 30 26
    Loop from residues 23-30 with the cutpoint at 26.
    
  3. Fragments file(s), as needed. Fragments are used in non-kic modes to speed sampling and capture local elements of secondary structure.

Command Lines and Options

  1. Sample Command:
    ./loopmodel.linuxgccrelease @flags 

  2. Options used in Loop Modeling

Result Interpretation

In general, the result structures' energies are interpreted as normal. Because loop modeling extensively remodels the backbone of the loops, you will want to pay special attention to rama (Ramachandran energy) and omega (related to the likelihood of a given omega [peptide bond] dihedral; statistics from the PDB). It may be worth examining per-residue scores within the loops as well, because single residues' bad ramas can significantly reduce the plausibility of a loop structure. CCD-style loop modeling also has a chainbreak term (usually called break or cbreak or chain) which measures how well the artificial chainbreak introduced for CCD closure was re-annealed.

The specifically important terms:

rama             Ramachandran energy (phi and psi dihedrals in the backbone)
omega            omega dihedral in the backbone
chainbreak       measures whether the loop was successfully closed.

Kinematic Loop Modeling

KIC modes use exact kinematic closure for loop buiding (perturb_kic) and/or refinement (refine_kic), and will not introduce chainbreaks. Omega angles, bond lengths, and non-N-CA-C bond angles remain fixed at their input values, or at canonical values if the "Extend loop" flag in the loop file is set to "1". N-CA-C bond angles are sampled within half a standard deviation from canonical values. Fragment files are not required/used in KIC modes.

KIC-specific loop modeling options


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