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AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking

Background: Computational analysis of protein-protein interaction provided the crucial information to increase the binding affinity without a change in basic conformation. Several docking programs were used to predict the near-native poses of the protein-protein complex in 10 top-rankings. The unive...

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Main Authors:	Wisitponchai, Tanchanok, Shoombuatong, Watshara, Lee, Vannajan Sanghiran, Kitidee, Kuntida, Tayapiwatana, Chatchai
Format:	Article
Published:	BioMed Central 2017
Subjects:	Q Science (General) QD Chemistry R Medicine
Online Access:	http://eprints.um.edu.my/22804/ https://doi.org/10.1186/s12859-017-1628-6
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spelling	my.um.eprints.228042019-10-22T04:08:48Z http://eprints.um.edu.my/22804/ AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking Wisitponchai, Tanchanok Shoombuatong, Watshara Lee, Vannajan Sanghiran Kitidee, Kuntida Tayapiwatana, Chatchai Q Science (General) QD Chemistry R Medicine Background: Computational analysis of protein-protein interaction provided the crucial information to increase the binding affinity without a change in basic conformation. Several docking programs were used to predict the near-native poses of the protein-protein complex in 10 top-rankings. The universal criteria for discriminating the near-native pose are not available since there are several classes of recognition protein. Currently, the explicit criteria for identifying the near-native pose of ankyrin-protein complexes (APKs) have not been reported yet. Results: In this study, we established an ensemble computational model for discriminating the near-native docking pose of APKs named "AnkPlex". A dataset of APKs was generated from seven X-ray APKs, which consisted of 3 internal domains, using the reliable docking tool ZDOCK. The dataset was composed of 669 and 44,334 near-native and non-near-native poses, respectively, and it was used to generate eleven informative features. Subsequently, a re-scoring rank was generated by AnkPlex using a combination of a decision tree algorithm and logistic regression. AnkPlex achieved superior efficiency with ≥1 near-native complexes in the 10 top-rankings for nine X-ray complexes compared to ZDOCK, which only obtained six X-ray complexes. In addition, feature analysis demonstrated that the van der Waals feature was the dominant near-native pose out of the potential ankyrin-protein docking poses. Conclusion: The AnkPlex model achieved a success at predicting near-native docking poses and led to the discovery of informative characteristics that could further improve our understanding of the ankyrin-protein complex. Our computational study could be useful for predicting the near-native poses of binding proteins and desired targets, especially for ankyrin-protein complexes. The AnkPlex web server is freely accessible at http://ankplex.ams.cmu.ac.th. BioMed Central 2017 Article PeerReviewed Wisitponchai, Tanchanok and Shoombuatong, Watshara and Lee, Vannajan Sanghiran and Kitidee, Kuntida and Tayapiwatana, Chatchai (2017) AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking. BMC Bioinformatics, 18 (1). p. 220. ISSN 1471-2105 https://doi.org/10.1186/s12859-017-1628-6 doi:10.1186/s12859-017-1628-6
institution	Universiti Malaya
building	UM Library
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Malaya
content_source	UM Research Repository
url_provider	http://eprints.um.edu.my/
topic	Q Science (General) QD Chemistry R Medicine
spellingShingle	Q Science (General) QD Chemistry R Medicine Wisitponchai, Tanchanok Shoombuatong, Watshara Lee, Vannajan Sanghiran Kitidee, Kuntida Tayapiwatana, Chatchai AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking
description	Background: Computational analysis of protein-protein interaction provided the crucial information to increase the binding affinity without a change in basic conformation. Several docking programs were used to predict the near-native poses of the protein-protein complex in 10 top-rankings. The universal criteria for discriminating the near-native pose are not available since there are several classes of recognition protein. Currently, the explicit criteria for identifying the near-native pose of ankyrin-protein complexes (APKs) have not been reported yet. Results: In this study, we established an ensemble computational model for discriminating the near-native docking pose of APKs named "AnkPlex". A dataset of APKs was generated from seven X-ray APKs, which consisted of 3 internal domains, using the reliable docking tool ZDOCK. The dataset was composed of 669 and 44,334 near-native and non-near-native poses, respectively, and it was used to generate eleven informative features. Subsequently, a re-scoring rank was generated by AnkPlex using a combination of a decision tree algorithm and logistic regression. AnkPlex achieved superior efficiency with ≥1 near-native complexes in the 10 top-rankings for nine X-ray complexes compared to ZDOCK, which only obtained six X-ray complexes. In addition, feature analysis demonstrated that the van der Waals feature was the dominant near-native pose out of the potential ankyrin-protein docking poses. Conclusion: The AnkPlex model achieved a success at predicting near-native docking poses and led to the discovery of informative characteristics that could further improve our understanding of the ankyrin-protein complex. Our computational study could be useful for predicting the near-native poses of binding proteins and desired targets, especially for ankyrin-protein complexes. The AnkPlex web server is freely accessible at http://ankplex.ams.cmu.ac.th.
format	Article
author	Wisitponchai, Tanchanok Shoombuatong, Watshara Lee, Vannajan Sanghiran Kitidee, Kuntida Tayapiwatana, Chatchai
author_facet	Wisitponchai, Tanchanok Shoombuatong, Watshara Lee, Vannajan Sanghiran Kitidee, Kuntida Tayapiwatana, Chatchai
author_sort	Wisitponchai, Tanchanok
title	AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking
title_short	AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking
title_full	AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking
title_fullStr	AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking
title_full_unstemmed	AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking
title_sort	ankplex: algorithmic structure for refinement of near-native ankyrin-protein docking
publisher	BioMed Central
publishDate	2017
url	http://eprints.um.edu.my/22804/ https://doi.org/10.1186/s12859-017-1628-6
_version_	1648736216011505664
score	13.211869

AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking

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