Residue Based

Analysis

Residue-based analysis consists of 4 analyses: SASA, Interface Label, Biophysical Type, and Energy. Residue Based is run by run_res_based function, which creates ResidueBased class. run_res_based gives 2 CSV files:

• residue_based_tbl.csv: Includes rASA monomer, rASA complex, delta rASA, Interface Label, SASA, Biophysical Type, Backbone Hbond, Sidechain Hbond, Van der Waals, Electrostatic, Total Energies in residue-based form, for each frame.

  • Interface Label: Integer values and corresponding values are as follows. For more information about this section, please have a look at the paper (Levy E., 2010)

    • 0: Interior

    • 1: Surface

    • 2: Support

    • 3: Rim

    • 4: Core

  • SASA: Calculated by dividing 100 the multiplications of relative SASA and Total SASA, in A^2. Calculated for each residue through the simulation.

  • Biophysical Type: Integer values and corresponding biophysical types are as follows:

    • 0: Hydrophobic

    • 1: Positively Charged

    • 2: Negatively Charged

    • 3: Polar

  • Energy Calculations: Energy calculations are run by FoldX. To run Residue Based analysis, the user must provide FoldX executable path. To install FoldX, please visit the FoldX site.

  • Secondary Structure: Runs the DSSP module according to the user's operating system and calculates the secondary structures of the residues for each frame. To run the DSSP, the user must use Linux/OsX or Windows Subsystem for Linux (WSL). To install the WSL, please visit https://learn.microsoft.com/en-us/windows/wsl/install .

  • SASA: The DynaBench calculates sasa according to the FreeSASA results. FreeSASA gives monomer SASA value as a percentage, which represents the solvent-accessible area of the residue in the monomer, meanwhile total SASA value (in monomer) of the residue is given as A^2. So, the DynaBench calculates the Solvent Accessible Area of the residue as:

$$SASA=(rASAm*rASAmTotal)/100$$

• interface_label_perc.csv: Includes residues with corresponding maximum conserved interface label and the percentage of the label conservation over the total simulation time.

DynaBench.dynabench.run_res_based(foldx_path, run_dssp=True)

• foldx_path: string, FoldX executable path.

• run_dssp: boolean, Run DSSP analysis if True, default is True.

Visualization

The visualization of Residue Based analysis is based on the files res_based_tbl.csv and interface_label_perc.csv. The Residue Based visualizations are Biophysical Type-Interface Label, Interface Residues' Interaction Energy, SASA, and DSSP plots.

DynaBench.Plotter.plot_biophys(path=None)

• path: string, Path of input file that includes Biophysical Type and Interface Label analysis data. If None, the function will search the res_based_tbl.csv file in the job_name/tables folder. The default is None.

DynaBench.Plotter.plot_SASA()

• Function does not accept arguments. When called, automatically plots the interface area trough simulation, in A^2.

DynaBench.Plotter.plot_DSSP(path=None, thereshold=50.0, intf_path=None)

DynaBench.Plotter.plot_int_energy(thereshold=50.0, intf_path=None, res_path=None
)

• thereshold: float, The threshold value to select interface residues. Percentage values below the threshold value in the interface_label_perc.csv (or another file in the same format if provided) will be counted as interface residue.

• intf_path: string, Path of the input file that includes interface labels and percentages. If None, the function will search the interface_label_perc.csv file in the job_name/tables folder. The default is None.

• res_path: string, Path of the input file that includes Energy analysis data. If None, the function will search the res_based_tbl.csv file in the job_name/tables folder. The default is None.