ArticleBriefings in bioinformatics2014
Evaluating template-based and template-free protein-protein complex structure prediction.
Article in Briefings in bioinformatics, 2014. 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.
- HawkDock version 2: an updated web server to predict and analyze the structures of protein-protein complexes.Nucleic acids research · 2025Article
- A multi-epitope self-amplifying mRNA SARS-CoV-2 vaccine design using a reverse vaccinology approach.Research in pharmaceutical sciences · 2024Article
- Review and Comparative Analysis of Methods and Advancements in Predicting Protein Complex Structure.Interdisciplinary sciences, computational life sciences · 2024Review
- Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Protein-protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction.RSC chemical biology · 2023Review
- Review
- Evolution as a Guide to DesigningInternational journal of molecular sciences · 2021Review
- Integrating ab initio and template-based algorithms for protein-protein complex structure prediction.Bioinformatics (Oxford, England) · 2020Article
- HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA.Nucleic acids research · 2019Article
- Prediction of Host-Pathogen Interactions for Helicobacter pylori by Interface Mimicry and Implications to Gastric Cancer.Journal of molecular biology · 2017Article
- SnapDock-template-based docking by Geometric Hashing.Bioinformatics (Oxford, England) · 2017Article
- Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks.BMC bioinformatics · 2017Article
- Template-Based Modeling of Protein-RNA Interactions.PLoS computational biology · 2016Article
- InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information.Nucleic acids research · 2016Article
- Progress and challenges in predicting protein interfaces.Briefings in bioinformatics · 2016Review
- Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.Journal of molecular biology · 2015Article
- Structural Modeling of GR Interactions with the SWI/SNF Chromatin Remodeling Complex and C/EBP.Biophysical journal · 2015Article
- Template-based prediction of protein function.Current opinion in structural biology · 2015Review
- PAIRpred: partner-specific prediction of interacting residues from sequence and structure.Proteins · 2014Article
- Template-based structure modeling of protein-protein interactions.Current opinion in structural biology · 2014Review
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4 authors.
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Abstract
We compared the performance of template-free (docking) and template-based methods for the prediction of protein-protein complex structures. We found similar performance for a template-based method based on threading (COTH) and another template-based method based on structural alignment (PRISM). The template-based methods showed similar performance to a docking method (ZDOCK) when the latter was allowed one prediction for each complex, but when the same number of predictions was allowed for each method, the docking approach outperformed template-based approaches. We identified strengths and weaknesses in each method. Template-based approaches were better able to handle complexes that involved conformational changes upon binding. Furthermore, the threading-based and docking methods were better than the structural-alignment-based method for enzyme-inhibitor complex prediction. Finally, we show that the near-native (correct) predictions were generally not shared by the various approaches, suggesting that integrating their results could be the superior strategy.
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