ArticleJournal of cheminformatics2017
HawkRank: a new scoring function for protein-protein docking based on weighted energy terms.
Article in Journal of cheminformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- HawkDock version 2: an updated web server to predict and analyze the structures of protein-protein complexes.Nucleic acids research · 2025Article
- Identification of a Novel Substrate for eEF2K and the AURKA-SOX8 as the Related Pathway in TNBC.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Evaluation of Structure Prediction and Molecular Docking Tools for Therapeutic Peptides in Clinical Use and Trials Targeting Coronary Artery Disease.International journal of molecular sciences · 2025Article
- A multi-epitope vaccine incorporating adhesin-derived antigens protects againstFrontiers in immunology · 2025Article
- Development of a multi-neoepitope vaccine targeting non-small cell lung cancer through reverse vaccinology and bioinformatics approaches.Frontiers in immunology · 2025Article
- Designing a multi-epitope subunit vaccine against Orf virus using molecular docking and molecular dynamics.Virulence · 2024Article
- Multi-epitope peptide vaccines targeting dengue virus serotype 2 created via immunoinformatic analysis.Scientific reports · 2024Article
- Unveiling the Binding between the Armadillo-Repeat Domain of Plakophilin 1 and the Intrinsically Disordered Transcriptional Repressor RYBP.Biomolecules · 2024Article
- Article
- Predictive Modeling and Structure Analysis of Genetic Variants in Familial Hypercholesterolemia: Implications for Diagnosis and Protein Interaction Studies.Current atherosclerosis reports · 2023Review
- MpbPPI: a multi-task pre-training-based equivariant approach for the prediction of the effect of amino acid mutations on protein-protein interactions.Briefings in bioinformatics · 2023Article
- Assessment of neutralization susceptibility of Omicron subvariants XBB.1.5 and BQ.1.1 against broad-spectrum neutralizing antibodies through epitopes mapping.Frontiers in molecular biosciences · 2023Article
- Rational strategies for enhancing mAb binding to SARS-CoV-2 variants through CDR diversification and antibody-escape prediction.Frontiers in immunology · 2023Article
- Article
- Immunoinformatics-guided designing and in silico analysis of epitope-based polyvalent vaccines against multiple strains of human coronavirus (HCoV).Expert review of vaccines · 2022Article
- Immunoinformatics Approach to Design Novel Subunit Vaccine against the Epstein-Barr Virus.Microbiology spectrum · 2022Article
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike.Translational medicine communications · 2022Article
- An Immunoinformatic Strategy to Develop NewInternational journal of peptide research and therapeutics · 2022Article
- In silico characterization, docking, and simulations to understand host-pathogen interactions in an effort to enhance crop production in date palms.Journal of molecular modeling · 2021Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Deciphering the structural determinants of protein-protein interactions (PPIs) is essential to gain a deep understanding of many important biological functions in the living cells. Computational approaches for the structural modeling of PPIs, such as protein-protein docking, are quite needed to complement existing experimental techniques. The reliability of a protein-protein docking method is dependent on the ability of the scoring function to accurately distinguish the near-native binding structures from a huge number of decoys. In this study, we developed HawkRank, a novel scoring function designed for the sampling stage of protein-protein docking by summing the contributions from several energy terms, including van der Waals potentials, electrostatic potentials and desolvation potentials. First, based on the solvation free energies predicted by the Generalized Born model for ~ 800 proteins, a SASA (solvent accessible surface area)-based solvation model was developed, which can give the aqueous solvation free energies for proteins by summing the contributions of 21 atom types. Then, the van der Waals potentials and electrostatic potentials based on the Amber ff14SB force field were computed. Finally, the HawkRank scoring function was derived by determining the most optimal weights for five energy terms based on the training set. Here, MSR (modified success rate), a novel protein-protein scoring quality index, was used to assess the performance of HawkRank and three other popular protein-protein scoring functions, including ZRANK, FireDock and dDFIRE. The results show that HawkRank outperformed the other three scoring functions according to the total number of hits and MSR. HawkRank is available at http://cadd.zju.edu.cn/programs/hawkrank .
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