CAMP: a Convolutional Attention-based Neural Network for Multi-level Peptide-protein Interaction Prediction
CAMP is a sequence-based deep learning framework for multifaceted prediction of peptide-protein interactions, including not only binary peptide-protein interactions, but also corresponding peptide binding residues.
cd ~/CAMP/data_prepare/
pdb_seqres.txt.gz --> pdb_seqres.txt
python .\step1_pdb_parse1.py
PLIP Dockerhub: https://hub.docker.com/r/pharmai/plip
docker pull pharmai/plip
docker run -v ${PWD}:/results -w /results pharmai/plip:latest -i 1A0M -t
histone H3 lysine 9 (PDB ID: 3QO2 [http://doi.org/10.2210/pdb3QO2/pdb])
T3 phosphorylated H3(1-15) peptide (PDB ID: 3UIG [http://doi.org/10.2210/pdb3UIG/pdb])
3IOL
4ZGM
Semaglutide-GlP-1R complex (PDB ID: 4ZGM [http://doi.org/10.2210/pdb4ZGM/pdb])
- 下载sequence和residues：crawl.py
- 生成peptide，receptor的target和query sequence
- 生成query的sequence vector: query_mapping.py
- 生成target的sequence vector：target_mapping.py
- 下载binding inter：download_inter.py
- 生成matrix:matrix.py