Adding Missing Residues

Briefs

Proteins are often missing residues from flexible loop regions. This is a problem for various types of calculations including molecular dynamics (MD) and quantum mechanics (QM) simulations. This function aids in HTP workflow design by adding missing Residue() objects into a Structure(). Missing residues can be defined by the user or by pulling from the Protein DataBank (PDB) when possible.

Note

Using this functionality requires the modeller python package to be installed. For more information on installing the package, see the Sali Lab website

Note

Science API is a special concept in EnzyHTP. They stands for those top-layer APIs the are supposed to be used in assembling the workflow.

Warning

Some loop refinement methods are known to slightly move sidechain positions. It may be necessary to minimize a Structure after filling in missing loops.

You will find a detailed tutorial of how to use this Science API.

Input/Output

dipole_bond

Input

The stru, missing_residues, method arguments and required inputs

  • stru:

    A Structure() object that is missing residues.

    Getting a Structure

    A Structure() object can be obtained using these APIs
  • missing_residues:

    A List[SeqRes] objects which describe the chain/index location and identity of each missing residue.

    Getting the missing residues

    A List[SeqRes] objects can be created by giving the four letter PDB code of a structure using the identify_missing_residues() function from the preparation module. (See tutorial here)
  • method:

    A str specifying the method to use for filling missing residues.

    Current method options

    At present, only modeller is supported.
  • work_dir:

    Working directory containing all the files in the calculation process. Optional argument.

  • inplace:

    Should the missing residues be added to the supplied Structure or to a new, copied one. Optional argument, True by default.

Output

A Union[None, Structure] that is either nothing or a copied Structure with the added missing residues.

Examples

Example Code

from enzy_htp import (
        PDBParser,
        identify_missing_residues,
        fill_missing_residues)

sp = PDBParser()

stru = sp.get_structure("./3r3v_.pdb")

print(stru)

fill_missing_residues(stru, identify_missing_residues("3R3V"))

print(stru)

The output from the above code is listed below:

<Structure object at 0x7f8576baa370>
Structure(
chains: (sorted, original ['A', 'B'])
    A(polypeptide): residue: 4-254,256-300 atom_count: 2339
    B(polypeptide): residue: 4-252,259-300 atom_count: 2310
)

<Structure object at 0x7f8576baa370>
Structure(
chains: (sorted, original ['A', 'B'])
    A(polypeptide): residue: -1-304 atom_count: 2408
    B(polypeptide): residue: -1-304 atom_count: 2408
)

Author: Chris Jurich <chris.jurich@vanderbilt.edu>