ArticlePloS one2013
Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.
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 6 papers.
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6 citing papers in PubMed.
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- Deciphering anti-colorectal cancer potential of Avicennia alba bioactives via network pharmacology and in vitro validation.Scientific reports · 2025Article
- Structural Insights Into Papain-Derived Synthetic Antibacterial Peptides for Targeting Klebsiella pneumoniae.Chemical biology & drug design · 2025Article
- Article
- Phytochemical characterization and anti-arthritic potential ofSaudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society · 2023Article
- Specificity of broad protein interaction surfaces for proteins with multiple binding partners.Biophysics and physicobiology · 2016Article
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Authors and funding
5 authors.
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Abstract
Interaction profile method is a useful method for processing rigid-body docking. After the docking process, the resulting set of docking poses could be classified by calculating similarities among them using these interaction profiles to search for near-native poses. However, there are some cases where the near-native poses are not included in this set of docking poses even when the bound-state structures are used. Therefore, we have developed a method for generating near-native docking poses by introducing a re-docking process. We devised a method for calculating the profile of interaction fingerprints by assembling protein complexes after determining certain core-protein complexes. For our analysis, we used 44 bound-state protein complexes selected from the ZDOCK benchmark dataset ver. 2.0, including some protein pairs none of which generated near-native poses in the docking process. Consequently, after the re-docking process we obtained profiles of interaction fingerprints, some of which yielded near-native poses. The re-docking process involved searching for possible docking poses in a restricted area using the profile of interaction fingerprints. If the profile includes interactions identical to those in the native complex, we obtained near-native docking poses. Accordingly, near-native poses were obtained for all bound-state protein complexes examined here. Application of interaction fingerprints to the re-docking process yielded structures with more native interactions, even when a docking pose, obtained following the initial docking process, contained only a small number of native amino acid interactions. Thus, utilization of the profile of interaction fingerprints in the re-docking process yielded more near-native poses.
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