ArticlePloS one2012
Protein docking by the interface structure similarity: how much structure is needed?
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Article
- GWYRE: A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes.Journal of molecular biology · 2022Article
- UDock2: interactive real-time multi-body protein-protein docking software.Bioinformatics (Oxford, England) · 2022Article
- DOCKGROUND membrane protein-protein set.PloS one · 2022Article
- Structural motifs in protein cores and at protein-protein interfaces are different.Protein science : a publication of the Protein Society · 2021Article
- How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking.Proteins · 2020Article
- ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking.Proteins · 2020Article
- Article
- Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking.Journal of computer-aided molecular design · 2018Article
- A Novel Geometry-Based Approach to Infer Protein Interface Similarity.Scientific reports · 2018Article
- Modeling CAPRI targets 110-120 by template-based and free docking using contact potential and combined scoring function.Proteins · 2018Article
- Dockground: A comprehensive data resource for modeling of protein complexes.Protein science : a publication of the Protein Society · 2018Article
- Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks.BMC bioinformatics · 2017Article
- The ClusPro web server for protein-protein docking.Nature protocols · 2017Article
- Template-Based Modeling of Protein-RNA Interactions.PLoS computational biology · 2016Article
- Structural templates for comparative protein docking.Proteins · 2015Article
- Evaluating template-based and template-free protein-protein complex structure prediction.Briefings in bioinformatics · 2014Article
- Template-based structure modeling of protein-protein interactions.Current opinion in structural biology · 2014Review
- Global and local structural similarity in protein-protein complexes: implications for template-based docking.Proteins · 2013Article
- Low-resolution structural modeling of protein interactome.Current opinion in structural biology · 2013Review
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3 authors.
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Abstract
The increasing availability of co-crystallized protein-protein complexes provides an opportunity to use template-based modeling for protein-protein docking. Structure alignment techniques are useful in detection of remote target-template similarities. The size of the structure involved in the alignment is important for the success in modeling. This paper describes a systematic large-scale study to find the optimal definition/size of the interfaces for the structure alignment-based docking applications. The results showed that structural areas corresponding to the cutoff values <12 Å across the interface inadequately represent structural details of the interfaces. With the increase of the cutoff beyond 12 Å, the success rate for the benchmark set of 99 protein complexes, did not increase significantly for higher accuracy models, and decreased for lower-accuracy models. The 12 Å cutoff was optimal in our interface alignment-based docking, and a likely best choice for the large-scale (e.g., on the scale of the entire genome) applications to protein interaction networks. The results provide guidelines for the docking approaches, including high-throughput applications to modeled structures.
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