ArticlePloS one2013
Exploring angular distance in protein-protein docking algorithms.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Performance of ZDOCK and IRAD in CAPRI rounds 39-45.Proteins · 2020Article
- Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking.Journal of molecular biology · 2018Article
- Performance of ZDOCK and IRAD in CAPRI rounds 28-34.Proteins · 2017Article
- cNMA: a framework of encounter complex-based normal mode analysis to model conformational changes in protein interactions.Bioinformatics (Oxford, England) · 2015Article
- Evaluating template-based and template-free protein-protein complex structure prediction.Briefings in bioinformatics · 2014Article
- Article
- Performance of ZDOCK in CAPRI rounds 20-26.Proteins · 2013Article
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3 authors.
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Abstract
We present a two-stage hybrid-resolution approach for rigid-body protein-protein docking. The first stage is carried out at low-resolution (15°) angular sampling. In the second stage, we sample promising regions from the first stage at a higher resolution of 6°. The hybrid-resolution approach produces the same results as a 6° uniform sampling docking run, but uses only 17% of the computational time. We also show that the angular distance can be used successfully in clustering and pruning algorithms, as well as the characterization of energy funnels. Traditionally the root-mean-square-distance is used in these algorithms, but the evaluation is computationally expensive as it depends on both the rotational and translational parameters of the docking solutions. In contrast, the angular distances only depend on the rotational parameters, which are generally fixed for all docking runs. Hence the angular distances can be pre-computed, and do not add computational time to the post-processing of rigid-body docking results.
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