Paper: Inter-chain contact map prediction for protein complex based on graph attention network and triangular multiplication update,Tong Wu, He Huang, Jiashan Li, Wenda Wang, GONG Xin-Qi. Abstract:
Residue-residue interactions between individual subunits of protein complexes are critical for predicting complex structures and can serve as distance constraints to guide complex structure modeling. Some recent studies have made some progress in predicting protein inter-chain contact maps based on multiple sequence alignments and deep learning models. Here we develop a new model based on graph attention network and triangular multiplication update to predict interchain contact maps for homologous protein complexes, named PGT (P is Protein, G is Graph attention network and T is Triangular multiplication update). Different from other methods which need to perform multiple sequence alignment processes and extract complicated manual features, PGT extracts embeddings of residues through the protein language model. Besides, we introduce structural information through the graph attention network to learn the spatial information of subunits from the complex structure and utilize the triangular multiplication module to capture triangular constraints between residues. To demonstrate the effectiveness of our method, we compare PGT with previous works such as DeepHomo, DRCon and Glinter on two independent test sets. The results show that PGT substantially outperforms these methods. Furthermore, we also perform two ablation experiments to demonstrate the necessity of introducing graph attention network and triangular multiplication update. In all, our framework presents new modules to accurately predict inter-chain contact maps in homologous protein complexes and it's also useful to analyze interactions in other type of protein complexes.
Introduction:
This is a program to predict inter-chain contact map for homologous protein complex , named PGT (P is Protein, G is Graph attention network and T is Triangular multiplication update).
Usage For Server:
You can click the [upload] button to submit a single pdb file or a zip file containing pdb files below, then click the [Submit] button. When your job-ID and input file display in the text box below, you can click the [Run] botton and wait for a while. Then you may click the [Check Result] button at intervals. When the [Click here to download] button appears below, you can proceed to download the result file. Otherwise, you may need to wait for a period of time or contact the Administrator of this website in Contact us. If you want to submit a new file, click the [Reset] button and repeat the steps above. The result file is a zip file. Note that the zip file includes different {pdb 's name}_result.txt files.
Get the Code & Dockerfile:
If you would like to download the source code, you can visit this website:
We recommend compiling PGT(and possibly its requirements) from the source code using the latest compiler for the best performace. You can also deploy PGT without building by Docker.Please note that PSAIA only supports Linux; for Windows users, please consider using WSL or docker.You can download the Dockerfile from here
Detailed Document For PGT:
If you would like to explore the usage details of PGT, you can read this document:
How to read the result file:
Since residue pair constraints can help to guide protein-protein docking and filter decoys with correct binding types, here we use the percentage of true positive contacts among the top 𝑁 predicted contacts to evaluate the results of our methods. In addition, we also evaluate the accuracy of 𝑡𝑜𝑝 𝐿/𝑘 (𝑘 =20) where 𝐿 is the length of one monomer of the homodimer. Note that the number "20" can be modified by yourself. The detailed interpretation of the result file is provided in the document here :
Contact us:
If you have any questions during operation, you can contact us through 13168zsl@ruc.edu.cn.
Try with Example:
We provide the example files below for you to try using the PGT server. The files include both a zip file which contains two dimers' pdb files.
Click [Upload file] and then input pdb name !
Click [Run] and Wait for a while then Click [Check Result] to Confirm that the program has finished computing.
