ArticleNucleic acids research2025
HawkDock version 2: an updated web server to predict and analyze the structures of protein-protein complexes.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
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- Immunoinformatic design of a multi-epitope vaccine candidate targeting multidrug-resistant Pseudomonas aeruginosa.BMC immunology · 2026Article
- From Sequence to Solution: Computational Design of a Multi-Epitope Vaccine Candidate Against Francisella tularensis.Probiotics and antimicrobial proteins · 2026Article
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- Macrophage FTO deficiency accelerates atherosclerosis via PACS2-mediated activation of the PPARγ lipid signaling pathway.Journal of translational medicine · 2026Article
- Genetic Polymorphisms Associated with Lithium Response in Bipolar Disorder: An Integrative Review and In Silico Protein-Protein Interaction Analysis.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Enhancing anticancer peptide discovery: A fusion-centric framework with conditional diffusion for prediction and generation.PLoS computational biology · 2026Article
- An integrated subtractive genomics and immunoinformatics approach for designing a universal multi-epitope vaccine againstFrontiers in bioinformatics · 2026Article
- Physics-Informed Artificial Intelligence Design of Picomolar Nanobodies Enables Deep Tumor Penetration and High-Contrast Imaging.Research (Washington, D.C.) · 2026Article
- Rational discovery of peptide inhibitors targeting Keap1: a focus on neurodegenerative diseases.Frontiers in bioinformatics · 2026Article
- Multimodal Learning of Protein-Protein Interactions for Accurate Binding Affinity Prediction.ACS omega · 2025Article
- Definition and Discovery of Tandem SH3-Binding Motifs Interacting with Members of the p47Biomolecules · 2025Article
- Factors Driving Amyloid Beta Fibril Recognition by Cell Surface Receptors: A Computational Study.Molecules (Basel, Switzerland) · 2025Article
- Pyruvate kinase M2 modulates Japanese encephalitis virus replication in neuronal cells.The Journal of general virology · 2025Article
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15 authors.
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Abstract
Protein-protein interactions (PPIs) are fundamental to cellular functions, yet predicting and analyzing their 3D structures remains a critical and computationally demanding challenge. To address this, the HawkDock web server was developed as an integrated computational platform for predicting and analyzing protein-protein complexes. Over the past 6 years, HawkDock has successfully processed >234 000 computational tasks. In this study, an updated version of HawkDock was developed with the following advancements: (1) a deep learning-based flexible docking method, GeoDock, has been integrated to improve docking accuracy, particularly for apo-protein structures; (2) the VD-MM/GBSA method, which outperforms conventional MM/GBSA approaches in predicting binding affinities, has been implemented; (3) a new Mutation Analysis Module has been added to systematically evaluate the energetic impacts of amino acid mutations on protein-protein binding; (4) the server has been migrated to a high-performance cluster with Amber upgraded to version 24. Here, we describe the general protocol of HawkDock2, with a particular focus on its new features related to flexible docking, VD-MM/GBSA affinity prediction, and amino acid residue mutations. Comprehensive validation studies have demonstrated the reliability and effectiveness of these new features. HawkDock2 will remain freely accessible to all users at http://cadd.zju.edu.cn/hawkdock/.
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