Global comparative structural analysis of responses to protein phosphorylation

Project on studying the structural effects of protein phosphorylation. Contains code for the manuscript Global comparative structural analysis of responses to protein phosphorylation.

Software requirements

OS requirements

The code has been run and tested on Linux (Ubuntu 20.04).

Python dependencies

The code was run on Python v3.10.13. The code depends on the following libraries (largely the standard Python scientific stack):

• numpy (used v1.23.4)
• scipy (used v1.9.3)
• numba (used v0.56.3)
• pandas (used v1.5.2)
• scikit-learn (used v1.2.0)
• tqdm (used v4.64.1)
• hdbscan (used v0.8.29)
• matplotlib (used v3.3.4)
• seaborn (used v0.12.2)
• biopython (used v1.76)
• prody (used v2.4.0)
• geometricus (used v0.1.2)
• PSA (used v1.1)

R dependencies

The code was run on R v4.4.1.

• bio3d (used v2.4-4)
• FSA (used v0.9.5)

External dependencies

• Clustal Omega (used v1.2.4)

Dataset

For convenience, some data is available in the repository (paired structures dataset, functional scores, UniProt site annotation...). Due to its size, the used structure data is available instead as a Zenodo repository.

Instructions

Individual scripts are typically set up to run on the data without the need for user input; instructions on the necessary inputs are otherwise provided as part of the documentation.

License

The code is available under the BSD-3 license. See the LICENSE file for details.

Citation

@article{correa2024global,
  title={Global comparative structural analysis of responses to protein phosphorylation},
  author={Correa Marrero, Miguel and Mello, Victor Hugo and Sartori, Pablo and Beltrao, Pedro},
  journal={bioRxiv},
  pages={2024--10},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}