Spatom is a state-of-the-art software to predict protein-protein interaction sites (PPIS). This program is for users to predict PPIS for protein with multiple polypeptide chains in unbound state.
This software is free to use, modify, redistribute without any restrictions, except including the license provided with the distribution.
Spatom can be used under both Linux and Windows environments. The Spatom is hosted on our webserver (http://118.190.151.48/Spatom/server).
Python 3.8.5
torch 1.10
torch-geometric 2.0.2
numpy 1.21.3
DSSP (user should install DSSP, the following command can be used to install DSSP)
$ conda install -c salilab dssp # for Linux
$ conda install -c speleo3 dssp # for Windows
freesasa 2.1.0
Biopython 1.7.9
sklean 0.23.2
If runing on GPU, Spatom needs
cuda 10.2
Spatom needs users to provide the files as follows.
- Providing PSSM
Please provide the PSSM files for all chains in PDB file, which should be named as proten_chain.pssm (e.g., 1A2K_A.pssm, 1A2K_B.pssm).
- Providing PDB
Spatom allows users to provide a protein PDB file, or just the protein name because Spatom can automatically download the corresponding PDB file.
usage: Spatom.py [-h] [--protein PROTEIN] [--PSSM PSSM] [--pdb PDB] [--output OUTPUT]
** Required **
--protein PROTEIN, -p PROTEIN protein name
--PSSM PSSM, -m PSSM path_to_PSSM_folder, save the PSSM files of corresponding chains into this folder
** Optional **
-h, --help show this help message and exit
--pdb PDB, -b PDB path_to_pdb/pdb_file
--output OUTPUT, -o OUTPUT path_to_output, defaut with path_to_Spatom-1.0/result
** Note **
Users must specify the '-p' item, i.e., protein's 4-letters PDB ID.
If the '-b' PDB item is empty in your command line, the corresponding PDB file will be downloaded automatically.
** Typical commands **
The following command is an example:
$ python ./Spatom-1.0/Spatom.py -p 1A2K -m ./Spatom-1.0/PSSM
The predicted result will be stored in output_path/predict_1A2K.txt.
Test data are provided with the software distribution in the ./sample_test directoriy.
a) change to the path_to_Spatom-1.0 directory
$ cd path_to_Spatom-1.0/
b) run Spatom
$ python Spatom.py -p 1A2K -m ./sample_test/PSSM -b ./sample_test/real_PDB/1A2K.pdb
Please check your PDB file first. If the PDB file misses some important atoms, please use a software (e.g. , PDBFixer) to fix it.
If you use this code, please cite
Haonan Wu, Jiyun Han, Shizhuo Zhang, Gaojia Xin, Chaozhou Mou, Juntao Liu, Spatom: a graph neural network for structure-based protein–protein interaction site prediction, Briefings in Bioinformatics, Volume 24, Issue 6, November 2023, bbad345, https://doi.org/10.1093/bib/bbad345
Any questions, problems, bugs are welcome and should be dumped to Haonan Wu [email protected].
Created on Dec. 15, 2022.