HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA
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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/.Keywords:
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Internet is a useful tool for all in a technologically advanced world. Internet use for education is very important. It is now in practice to teach school to college to get more out of it. In this study, the emphasis is given on the most important success factor that investigates about Internet usage by students of the University, whether it is an effective learning tool for students and teachers and also examines the level of use Internet and whether the Internet is useful for distance learners. The sample of the data is taken from the universities of the twin cities (Islamabad and Rawalpindi). The quantitative technique for data analysis was SPSS. The results reveal that most students find that the Internet knowledge is essential for students and teachers. Above all respondents in the questionnaire that students feel comfortable using the Internet and provides substantial information and half of those surveyed felt that Internet use is difficult in school. Results show that the Internet is easier to use then the collection of research tools, while the Internet is very important. It is recommended that students should align their potential for significant and positive use of the Internet. Further it is recommended also to educate students to use basic Internet tools.
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