Improving protein-protein interaction site prediction using Graph Neural Network and structure profiles
NCBI nr database (https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/)
- Install psiblast in order to calculate PSSM embeddings
- Install bio_embeddings packege in order to calculate T5 embeddings
- Refer to requirements for environment dependencies. (such as Pytorch and DGL installation)
Download this repository at bukkeshuo/TargetPPI for academic use. Then, uncompress it and run the following command lines on Linux System.
$ cd xxxx/ TargetPPI
$ python predecit.py xxxx
The Results directory encompass the predictions utilized in this paper. This directory contains the outputs of the methods employed in the research study, which were then utilized to draw conclusions. By putting the predictions in the Result directory, the researchers can easily access and analyze them for further investigation and evaluation.