DCA Frustratometer examples

Loading Protein Structures

The Frustratometer package includes a prody-based Structure class to load the structure and calculate the properties needed for the AWSEM and DCA Frustratometers.

import frustratometer

# Define the path to your PDB file
pdb_path = Path('data/my_protein.pdb')
# Load the structure
structure = frustratometer.Structure.full_pdb(pdb_path)
structure.sequence #The sequence of the structure

Creating a DCA Model Instance

After loading the structure, create a DCA model instance with the desired parameters. When creating a DCA model instance, you can provide an existing Potts model or a Potts model file (in Matlab format). Additionally, the Frustratometer can generate a Potts model for a given protein via the pydca package.

When using Potts Model files generated by the mfDCA algorithm, make sure to set the “reformat_potts_model” to True.

Check the Accuracy of the Potts Model

In order to check the accuracy of the contacts predicted by the Potts model and true contacts from the protein’s contact map, the receiver operator curve (ROC) can be generated. If the Potts model has high accuracy, the Area Under the Curve (AUC) of the ROC will be 1.

Calculating Frustration Indices

Frustration indices can be calculated for single residues or mutationally. This measurement helps identify energetically favorable or unfavorable interactions within the protein structure.

Single Residue Frustration

# Calculate single residue frustration
single_residue_frustration = model_dca.frustration(kind='singleresidue')
print(single_residue_frustration)

Single Residue Decoy Fluctuation

The frustratometer package also allows the quick calculation of the energies of all single residue and mutational decoys.

# Calculate mutational frustration
mutational_frustration = model_dca.decoy_fluctuation(kind='singleresidue')
print(mutational_frustration)

Mutational Frustration

# Calculate mutational frustration
mutational_frustration = model_dca.frustration(kind='mutational')
print(mutational_frustration)

Energy Calculations

You can calculate different energy contributions, including fields energy (pseudo one-body terms like burial), couplings energy (pseudo two-body terms like contact and electrostatics), and their combination to determine the native energy of the protein structure. The fields, couplings, and native energies of other threaded sequences can be calculated like below by simply changing the “sequence” variable in the functions’ arguments.

Fields Energy

fields_energy = model_dca.fields_energy()
print(fields_energy)

Couplings Energy

couplings_energy = model_dca.couplings_energy()
print(couplings_energy)

Native Energy

Native energy can be considered as a combination of fields and couplings energy contributions.

native_energy = model_dca.native_energy()
print(native_energy)