The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA
Open accessAbstract
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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CAPRI: A Critical Assessment of PRedicted Interactions
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Protein-Protein Docking: From Interaction to Interactome
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“Therefore, determination of their complex structures is critical to understand the underlying molecular mechanisms of crucial biological processes (1) and even design compounds that interfere with PPIs with pharmaceutical significance (2).”
BackgroundCorrada, D., Soshilov, A. A., Denison, M. S., & Bonati, L. (2016) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004981 · Cited by 43
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Breaching the Bacterial Envelope: The Pivotal Role of Perforin-2 (MPEG1) Within Phagocytes
Merselis, L. C., Rivas, Z. P., & Munson, G. P. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.597951 · Cited by 18
Murmu, S., Rashmi, M., Nagrale, D. T., Kour, T., Singh, M. K., Chaurasia, A., Behera, S. K., Shankar, R., Ranjan, R., Jha, G. K., et al. (2025) · Journal of Cotton Research · doi:10.1186/s42397-024-00203-z · Cited by 7
Ruiz-Molina, N., Parsons, J., Decker, E. L., & Reski, R. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.02.002 · Cited by 4
Improved antibody-specific epitope prediction using AlphaFold and AbAdapt
Xu, Z., Davila, A., Wiamowski, J., Teraguchi, S., & Standley, D. M. (2022) · doi:10.1101/2022.05.21.492907 · Cited by 4
Computational Design of a TCR-Based Bispecific Engager Targeting Cancerous KRAS G12V Mutations
Shah, N., Sharma, G., Patel, V., Wu, M., Mummadi, A., Taneja, A., Shah, M., Le, G. B., Krishna, M., & Brah, H. (2026) · ACS Omega · doi:10.1021/acsomega.5c10229
Mukhtar, O., Dutt, R., Panda, A., Kumari, P., Singh, S. S., Paul, G., Prakash, N., Abbas, M., Islam, M. M., Arora, P., et al. (2026) · eLife · doi:10.7554/elife.110942
Metadata
- Authors
- Weng, G., Wang, E., Wang, Z., Liu, H., Zhu, F., Li, D., & Hou, T.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-05-20
- Volume
- 47
- Issue
- W1
- Pages
- W322-W330
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2945172910
- Cited by
- 637
- References
- 4
- FWCI
- 16.76
- Type
- journal article
- Language
- en
- Open access
- gold
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