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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| Format: | Article |
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BioMed Central
2017
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| 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 |
| collection | UM |
| 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. |
| first_indexed | 2024-03-06T05:58:03Z |
| format | Article |
| id | um.eprints-22804 |
| institution | Universiti Malaya |
| last_indexed | 2024-03-06T05:58:03Z |
| publishDate | 2017 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | 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, DOI https://doi.org/10.1186/s12859-017-1628-6 <https://doi.org/10.1186/s12859-017-1628-6>. https://doi.org/10.1186/s12859-017-1628-6 doi:10.1186/s12859-017-1628-6 |
| 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 |
| title | 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_short | AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking |
| title_sort | ankplex algorithmic structure for refinement of near native ankyrin protein docking |
| topic | Q Science (General) QD Chemistry R Medicine |
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