Paper Info
Title
HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA.
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 similar to 81.4% predicted models and similar to 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/.
Year
DOI
Venue
2019
10.1093/nar/gkz397
NUCLEIC ACIDS RESEARCH
DocType
Volume
Issue
Journal
47
W1
ISSN
Citations 
PageRank 
0305-1048
1
0.36
References 
Authors
0
7
Name
Order
Citations
PageRank
Gaoqi Weng122.06
Ercheng Wang242.48
Zhe Wang311.71
Hui Liu432.11
Feng Zhu513414.75
Dan Li6266.82
Tingjun Hou742754.50