ArticleNucleic acids research2019
HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 314 papers.
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314 citing papers in PubMed.
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- Computational Study of Antibody Binding to SARS-CoV-2 Variants.Antibodies (Basel, Switzerland) · 2026Article
- RNase A is inhibited by the cysteine-rich protein thionein but not by the metal-containing form metallothionein.Molecular and cellular biochemistry · 2026Article
- Copper(II) benzyloxychalcone analogues as new potential metallodrugs against SARS-CoV-2 replication.The Journal of general virology · 2026Article
- Mechanisms of Binding and Immune Escape Resistance for Broadly Neutralizing Antibodies Targeting Distinct Conserved SARS-CoV-2 Spike Epitopes: A Hierarchical Approach Integrating Mutational Profiling and Energy Landscape Analysis.International journal of molecular sciences · 2026Article
- Computational design of a multi-epitope vaccine against Helicobacter pylori targeting CagA, FliD, urease, and OipA with cholera toxin B subunit (CTB) adjuvant.BMC microbiology · 2026Article
- Spatial transcriptomic atlas of murine neurotoxocariasis reveals region-specific host responses and dysfunction in the brain.Nature communications · 2026Article
254 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
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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/.
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