Loop Modeling Application

This release of Rosetta3 includes updates to the Rosetta 2.x cyclic coordinate descent loop modeling. 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/.

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 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 kill 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.

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