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. 2019 Jul 2;47(W1):W322-W330.
doi: 10.1093/nar/gkz397.

HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA

Gaoqi Weng  1 , Ercheng Wang  1 , Zhe Wang  1 , Hui Liu  1 , Feng Zhu  1 , Dan Li  1 , Tingjun Hou  1   2
Affiliations

HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA

Gaoqi Weng et al. Nucleic Acids Res. .

Abstract

Protein-protein interactions (PPIs) play an important role in the different functions of cells, but accurate prediction of the three-dimensional structures for PPIs is still a notoriously difficult task. In this study, HawkDock, a free and open accessed web server, was developed to predict and analyze the structures of PPIs. In the HawkDock server, the ATTRACT docking algorithm, the HawkRank scoring function developed in our group and the MM/GBSA free energy decomposition analysis were seamlessly integrated into a multi-functional platform. The structures of PPIs were predicted by combining the ATTRACT docking and the HawkRank re-scoring, and the key residues for PPIs were highlighted by the MM/GBSA free energy decomposition. The molecular visualization was supported by 3Dmol.js. For the structural modeling of PPIs, HawkDock could achieve a better performance than ZDOCK 3.0.2 in the benchmark testing. For the prediction of key residues, the important residues that play an essential role in PPIs could be identified in the top 10 residues for ∼81.4% predicted models and ∼95.4% crystal structures in the benchmark dataset. To sum up, the HawkDock server is a powerful tool to predict the binding structures and identify the key residues of PPIs. The HawkDock server is accessible free of charge at http://cadd.zju.edu.cn/hawkdock/.

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Figures

Figure 1.
Figure 1.
Workflow of the HawkDock server that is divided into three major steps: (i) input of unbound or bound protein structures; (ii) structural prediction of protein–protein complex by using the global docking algorithm implemented in ATTRACT and the HawkRank scoring function; (iii) identification of the key residues by MM/GBSA.
Figure 2.
Figure 2.
Data input in the HawkDock server. (A) A HawkDock job needs: (1) optional job name and email address, (2) PDB files or PDB IDs, (3) optional distance restraints, (4) optional MM/GBSA re-scoring, (5) the ‘submit’ button and (6) the log of the HawkDock job. (B) A MM/GBSA job needs: (1) optional job name and email address, (2) PDB file or PDB ID, (3) the chain IDs of receptor and ligand, (4) the ‘submit’ button and (5) the log of the MM/GBSA job.
Figure 3.
Figure 3.
The result pages of HawkDock and MM/GBSA. (A) At the top left of the page is (1) the job name, and under it are (2) the files for downloading. (3) A summary of the docking scores for the top 10 models is presented on the left bottom. (4) The top 10 models can be viewed in 3Dmol.js with (5) the optional buttons to control which model to display. (6) The table summarizes the submission and results of MM/GBSA and (7) the brief instructions are shown on the bottom. (B) At the top of page is (1) the job name, and under it is (2) the value of the binding free energy and (3) the files for downloading. The per-residue free energy contributions ordered from largest to smallest for (4) receptor and (5) ligand are displayed in the table, (6) through which the users can choose which residue to display in 3Dmol.js. (7) The brief instructions are also displayed on the bottom.
Figure 4.
Figure 4.
(A) The success rates from top 10 to top 1000 and top 1 to top 10 of HawkDock, ATTRACT, and ZDOCK 3.0.2, and (B) the success rates of the key residues predicted by MM/GBSA.
Figure 5.
Figure 5.
The structural alignment of the crystal structure (PDB ID: 3D5S) colored yellow and the theoretical model predicted by HawkDock (colored green).
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References

    1. Gress A., Ramensky V., Kalinina O.V.. Spatial distribution of disease-associated variants in three-dimensional structures of protein complexes. Oncogenesis. 2017; 6:e380. - PMC - PubMed
    1. Vakser I.A. Protein-protein docking: from interaction to interactome. Biophys. J. 2014; 107:1785–1793. - PMC - PubMed
    1. Vreven T., Hwang H., Pierce B.G., Weng Z.. Evaluating template-based and template-free protein–protein complex structure prediction. Brief. Bioinform. 2014; 15:169–176. - PMC - PubMed
    1. Aloy P., Ceulemans H., Stark A., Russell R.B.. The relationship between sequence and interaction divergence in proteins. J. Mol. Biol. 2003; 332:989–998. - PubMed
    1. de Vries S.J., Schindler C.E., Chauvot de Beauchene I., Zacharias M.. A web interface for easy flexible protein–protein docking with ATTRACT. Biophys. J. 2015; 108:462–465. - PMC - PubMed

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