FoldX extension to homelette
Philipp Junk, 2021
This extension contains evaluation metrics based on FoldX, a force field for energy calculation and protein design (https://foldxsuite.crg.eu/) 1 2.
- 1
Guerois, R., Nielsen, J. E., & Serrano, L. (2002). Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of More Than 1000 Mutations. Journal of Molecular Biology, 320(2), 369–387. https://doi.org/10.1016/S0022-2836(02)00442-4
- 2
Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., & Serrano, L. (2005). The FoldX web server: an online force field. Nucleic Acids Research, 33(Web Server), W382–W388. https://doi.org/10.1093/nar/gki387
Usage
import homelette.extension.extension_foldx as extension_foldx
help(extension_foldx.Evaluation_foldx_stability)
This extension expects FoldX to be installed and in your path.
Functions and classes
- Currently contains the following items:
Evaluation_foldx_repairmodels
Evaluation_foldx_interaction
Evaluation_foldx_stability
Evaluation_foldx_alascan_buildmodels
Evaluation_foldx_alascan_interaction
-
class
homelette.extension.extension_foldx.
Evaluation_foldx_repairmodels
(model, quiet=False) Creates a modified version of the PDB and runs RepairPDB on it
Will not dump an entry to the model.evaluation dictionary
- Parameters
model (Model) – The model object to evaluate
quiet (bool) – If True, will perform evaluation with suppressing stdout (default False). Needs to be False for running it asynchronously, as done when running Task.evaluate_models with multple cores
- Variables
model (Model) – The model object to evaluate
output (dict) – Dictionary that all outputs will be dumped into
Notes
Most PDBs work fine with FoldX. For a specific use case in which I was working with GTP heteroatoms, I had to rename a few atoms to make the PDB compliant with FoldX.
-
evaluate
() Repairs models with FoldX. Automatically called on object initialization
- Returns
- Return type
None
-
class
homelette.extension.extension_foldx.
Evaluation_foldx_interaction
(model, quiet=False) Calculates interaction energy with FoldX
Requires a protein-protein complex. Expects Evaluation_foldx_repairmodels to have been performed beforehand.
Will dump the following entries to the model.evaluation dictionary:
foldx_interaction
- Parameters
model (Model) – The model object to evaluate
quiet (bool) – If True, will perform evaluation with suppressing stdout (default False). Needs to be False for running it asynchronously, as done when running Task.evaluate_models with multple cores
- Variables
model (Model) – The model object to evaluate
output (dict) – Dictionary that all outputs will be dumped into
-
evaluate
() Calculates protein interaction energy with FoldX. Automatically called on object initialization.
- Returns
- Return type
None
-
class
homelette.extension.extension_foldx.
Evaluation_foldx_stability
(model, quiet=False) Calculate protein stability with FoldX
Expects Evaluation_foldx_repairmodels to have been performed beforehand.
Will dump the following entries to the model.evaluation dictionary:
foldx_stability
- Parameters
model (Model) – The model object to evaluate
quiet (bool) – If True, will perform evaluation with suppressing stdout (default False). Needs to be False for running it asynchronously, as done when running Task.evaluate_models with multple cores
- Variables
model (Model) – The model object to evaluate
output (dict) – Dictionary that all outputs will be dumped into
-
evaluate
() Calculates protein stability with FoldX. Automatically called on object initialization.
- Returns
- Return type
None
-
class
homelette.extension.extension_foldx.
Evaluation_foldx_alascan_buildmodels
(model, quiet=False) Generates alanine point mutations for all positions in the given model using FoldX. Automatically called on object initialization.
Expects Evaluation_foldx_repairmodels to have been performed beforehand.
Will not dump an entry to the model.evaluation dictionary.
- Parameters
model (Model) – The model object to evaluate
quiet (bool) – If True, will perform evaluation with suppressing stdout (default False). Needs to be False for running it asynchronously, as done when running Task.evaluate_models with multple cores
- Variables
model (Model) – The model object to evaluate
output (dict) – Dictionary that all outputs will be dumped into
See also
Notes
This Evaluation is very RAM intensive, so expect only to run 1 or 2 threads ni parallel.
-
evaluate
() Generates alanine point mutations for all positions in the given model. Automatically called on object initialization.
- Returns
- Return type
None
-
class
homelette.extension.extension_foldx.
Evaluation_foldx_alascan_interaction
(model, quiet=False) Calculates protein interaction energy with FoldX for all alanine point mutations generated by Evaluation_foldx_alascan_buildmodels.
Expects Evaluation_foldx_alascan_buildmodels to have been run before.
Will dump the following entry to the model.evaluation dictionary:
- foldx_alascan: Dictionary of all interaction energies for all alanine
scan mutations.
- Parameters
model (Model) – The model object to evaluate
quiet (bool) – If True, will perform evaluation with suppressing stdout (default False). Needs to be False for running it asynchronously, as done when running Task.evaluate_models with multple cores
- Variables
model (Model) – The model object to evaluate
output (dict) – Dictionary that all outputs will be dumped into
See also
-
evaluate
() Calculates protein interaction energy with FoldX for all alanine point mutations generated by Evaluation_foldx_alascan_buildmodels.
- Returns
- Return type
None