Paper: Division of Protein Surface Patches and Its Application in Protein Binding Site Prediction,WANG Pan-Wen, GONG Xin-Qi, LI Chun-Hua, CHEN Wei-Zu, WANG Cun-Xin. Abstract:
Binding site prediction for protein-protein complexes is a challenging problem in the area of computational molecular biology. Using a set of double-chain complexes in Benchmark 3.0, we calculated the solvent accessible surface areas and inter-residue contact areas for each monomer and propose a division method of protein surface patches. We found that the products of the solvent accessible surface areas and internal contact areas of patches, the PSAIA values, could provide protein binding site information. In a dataset of 78 complexes, either receptors or ligands of 74 complexes had interface patches with the first or second greatest PSAIA values among all surface patches. A good docking result was achieved when the binding site information obtained with this method was applied in Target 39 of the CAPRI experiment. This patch-based protein binding site prediction method differs from traditional methods, which are based on single residue and consider only surface residues. This provides a new method for binding site prediction in protein-protein interactions.
Introduction:
This is a online server to calculate PSAIA of proteins and then give a series of residue patchs which may contain possible binding sites of proteins.
Usage For Server: [NOTICE]: you must input your email address in the [email] textarea to receive the results !! Then 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 email address, job-ID and input file display in the text box below, you can click the [Run] botton and wait for a while. 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 PSAIA(and possibly its requirements) from the source code using the latest compiler for the best performace. You can also deploy PSAIA 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 PSAIA:
If you would like to explore the usage details of PSAIA, you can read this document:
How to read the result file:
We divide the results based on each chain of the protein and select the top 15 highest-scoring patches in each chain.These patches are considered to be the most likely to contain protein binding sites. Note that the number "15" 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 2021103691@ruc.edu.cn.
Try with Example:
We provide the example files below for you to try using the PSAIA server. The files include both a zip file which contains two dimers' pdb files and three dimers' pdb files.
You must provide your email address to receive the results !!! Then Click [Upload file] and then Click [Submit] !
