ArticleProteins2015
Structural templates for comparative protein docking.
Article in Proteins, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.Proteins · 2023Article
- Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.Proteomics · 2023Article
- Structural motifs in protein cores and at protein-protein interfaces are different.Protein science : a publication of the Protein Society · 2021Article
- Quality Assessment of Protein Docking Models Based on Graph Neural Network.Frontiers in bioinformatics · 2021Article
- Protein Docking Model Evaluation by Graph Neural Networks.Frontiers in molecular biosciences · 2021Article
- Application of docking methodologies to modeled proteins.Proteins · 2020Article
- How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking.Proteins · 2020Article
- Protein docking model evaluation by 3D deep convolutional neural networks.Bioinformatics (Oxford, England) · 2020Article
- Article
- Efficient flexible backbone protein-protein docking for challenging targets.Bioinformatics (Oxford, England) · 2018Article
- 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
- Improved performance in CAPRI round 37 using LZerD docking and template-based modeling with combined scoring functions.Proteins · 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
- SnapDock-template-based docking by Geometric Hashing.Bioinformatics (Oxford, England) · 2017Article
- Modeling complexes of modeled proteins.Proteins · 2017Article
- Structural quality of unrefined models in protein docking.Proteins · 2017Article
- Assessment of refinement of template-based models in CASP11.Proteins · 2016Article
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4 authors.
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Abstract
Structural characterization of protein-protein interactions is important for understanding life processes. Because of the inherent limitations of experimental techniques, such characterization requires computational approaches. Along with the traditional protein-protein docking (free search for a match between two proteins), comparative (template-based) modeling of protein-protein complexes has been gaining popularity. Its development puts an emphasis on full and partial structural similarity between the target protein monomers and the protein-protein complexes previously determined by experimental techniques (templates). The template-based docking relies on the quality and diversity of the template set. We present a carefully curated, nonredundant library of templates containing 4950 full structures of binary complexes and 5936 protein-protein interfaces extracted from the full structures at 12 Å distance cut-off. Redundancy in the libraries was removed by clustering the PDB structures based on structural similarity. The value of the clustering threshold was determined from the analysis of the clusters and the docking performance on a benchmark set. High structural quality of the interfaces in the template and validation sets was achieved by automated procedures and manual curation. The library is included in the Dockground resource for molecular recognition studies at http://dockground.bioinformatics.ku.edu.
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