SimBa2 is a Python package for predicting changes in protein stability upon mutation using the prediction methods SimBa-IB and SimBa-SYM. The program retrieves a PDB structure from RCSB PDB or takes a local PDB file as input, and outputs the predicted stability changes (ΔΔG; in kcal/mol) for all possible single amino acid changes.
Negative ΔΔG values signify destabilizing mutations.
The program can be run from the command line or used as a Python module.
python -m pip install https://github.com/kasperplaneta/SimBa2/archive/main.tar.gz
The program takes a single PDB code or a local PDB file as input, and outputs two .csv files (SimBa-IB_<pdb-code>.csv and SimBa-SYM_<pdb-code>.csv) with predicted ddG values in kcal/mol for a saturated mutagenesis of the protein.
Analyze PDB structure 3BDN:
python -m simba2 3bdn
Keep downloaded PDB file in the current directory:
python -m simba2 3bdn --keep
Keep downloaded PDB file in another directory:
python -m simba2 3bdn --dir ../my_directory --keep
Analyze local PDB file of 3BDN:
python -m simba2 3bdn --file 3bdn.pdb
Help:
python -m simba2 --help
The package can also be used as a module in a Python script to analyze local PDB files.
Example:
from simba2 import methods as sb
sb.simba2_predict('3BDN', '3bdn.pdb')
The package so far only works with structures that are available in PDB format, not mmCIF format.
The resulting .csv files (or dataframe when used in a Python script) have mostly self-explanatory column names.
The column named mean_RSA shows the mean RSA value across chains if the structure is a homooligomer (this is defined using the sequence in the PDB's SEQRES record. If no SEQRES record is present, mean_RSA will not be calculated, even if the structure is a homooligomer).
Please acknowledge the use of SimBa2 by citing the following publication:
Bæk, K. T. and K. P. Kepp (2022) Data set and fitting dependencies when estimating protein mutant stability: Toward simple, balanced, and interpretable models. J Comput Chem. https://doi.org/10.1002/jcc.26810
The MIT License (MIT)
Copyright (c) 2021 Kristoffer Torbjørn Bæk, Kasper Planeta Kepp, Technical University of Denmark
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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