ArticleProteins2022
Benchmarking of structure refinement methods for protein complex models.
Article in Proteins, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Immunoinformatics-driven multi-epitope vaccine design as a promising strategy against multidrug-resistant pathogens: a comprehensive review.Folia microbiologica · 2026Review
- Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process.Bioinformatics advances · 2023Article
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2 authors.
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Abstract
Protein structure docking is the process in which the quaternary structure of a protein complex is predicted from individual tertiary structures of the protein subunits. Protein docking is typically performed in two main steps. The subunits are first docked while keeping them rigid to form the complex, which is then followed by structure refinement. Structure refinement is crucial for a practical use of computational protein docking models, as it is aimed for correcting conformations of interacting residues and atoms at the interface. Here, we benchmarked the performance of eight existing protein structure refinement methods in refinement of protein complex models. We show that the fraction of native contacts between subunits is by far the most straightforward metric to improve. However, backbone dependent metrics, based on the Root Mean Square Deviation proved more difficult to improve via refinement.
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