Paper: Predicting Interface Residues for Protein Polymers Based on Module Division,Shuhong Yu, Zicheng Xie, Jiudong Wang, Xinqi Gong. Abstract
In the field of computational biology, AlphaFold has made remarkable progress in predicting protein struc-
tures. However, for some multimeric complexes, the accuracy of its predictions still needs to be improved.
Enhancing the prediction of binding sites in protein oligomers contributes to the prediction of overall struc-
tures, and the details of binding sites are crucial for understanding the functional mechanism, affinity, and
specificity of complexes. The approach presented here is independent of black-box modeling, thereby facilitat-
ing a clearer elucidation of the underlying biological mechanisms of protein-protein interaction interfaces. The
study investigates protein interaction sites mainly for trimers and tetramers in the PDB database, using a
modular division method. By ranking modules based on the SSAIA (a linear combination of the square of the
solvent-accessible surface area and the internal contact area) value, it was found that interface modules are
more likely to appear in surface modules with lower SSAIA values. Among 44,964 monomers, 92.25% of the
monomer interface residues are found in the three modules with the smallest SSAIA values. In 5,240 trimers,
98.63% of the complexes have at least one chain correctly predicted, and in 7,311 tetramers, 98.92% of the
complexes have at least one chain correctly predicted, with an average of approximately 3 out of 4 residues
in the top-ranked interface modules being interface residues. The comparison results with other methods in
Benchmark 2.0 dataset and 12 targets of the CASP15 competition have validated the effectiveness of our ap-
proach, providing a new perspective for the prediction of binding sites in multimer interactions. Utilizing the
method presented in this article, we have provided a server for scholars to predict protein interaction interfaces
at http://mialab.ruc.edu.cn/PAMA3Server/, and the PDB code used in this work can also be obtained.
Introduction:
PAMA3 server is a online server to calculate SSAIA of proteins and then give a series of residue
patches which may contain possible binding sites of protein polymers, mainly for dimers, trimer and tetramers.
Interested readers can try to use the server we provide to predict
the interface residues of multimeric proteins with more than four chains. Note that we are unable to predict proteins with the number
of monomer residues exceeding 1,000.
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 (For each PDB entered, the corresponding {pdb 's name}_result.txt file is returned in the zip file).
Get the Code:
If you would like to download the source code, you can visit this website:
How to read the result file:
In the {pdb 's name}_result.txt file, we divide the results based on each chain of the protein, we give the number of surface modules of each chain, the number of interface modules and the highest rank of interface modules on the chain(Rank). And we provide the top 5 highest ranking patches in each chain, including residue numbers, amino acid names, and chain names. These patches are considered to be the most likely to contain protein binding sites.
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 PAMA3 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] !
