Narrow funnel-like interaction energy distribution is an indicator of specific protein interaction partner
Summary: Protein interaction networks underlie countless biological mechanisms. However, most protein interaction predictions are based on biological evidence that are biased to well-known protein interaction or physical evidence that exhibits low accuracy for weak interactions and requires high com...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-06-01
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| Series: | iScience |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004223009884 |
| _version_ | 1827934675505512448 |
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| author | Juyoung Choi |
| author_facet | Juyoung Choi |
| author_sort | Juyoung Choi |
| collection | DOAJ |
| description | Summary: Protein interaction networks underlie countless biological mechanisms. However, most protein interaction predictions are based on biological evidence that are biased to well-known protein interaction or physical evidence that exhibits low accuracy for weak interactions and requires high computational power. In this study, a novel method has been suggested to predict protein interaction partners by investigating narrow funnel-like interaction energy distribution. In this study, it was demonstrated that various protein interactions including kinases and E3 ubiquitin ligases have narrow funnel-like interaction energy distribution. To analyze protein interaction distribution, modified scores of iRMS and TM-score are introduced. Then, using these scores, algorithm and deep learning model for prediction of protein interaction partner and substrate of kinase and E3 ubiquitin ligase were developed. The prediction accuracy was similar to or even better than that of yeast two-hybrid screening. Ultimately, this knowledge-free protein interaction prediction method will broaden our understanding of protein interaction networks. |
| first_indexed | 2024-03-13T07:43:07Z |
| format | Article |
| id | doaj.art-b4ac782ab2af4b4a80aec2f87dce67ab |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-03-13T07:43:07Z |
| publishDate | 2023-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-b4ac782ab2af4b4a80aec2f87dce67ab2023-06-03T04:22:31ZengElsevieriScience2589-00422023-06-01266106911Narrow funnel-like interaction energy distribution is an indicator of specific protein interaction partnerJuyoung Choi0Department of Life Science, Sogang University, Seoul 04017, South Korea; Corresponding authorSummary: Protein interaction networks underlie countless biological mechanisms. However, most protein interaction predictions are based on biological evidence that are biased to well-known protein interaction or physical evidence that exhibits low accuracy for weak interactions and requires high computational power. In this study, a novel method has been suggested to predict protein interaction partners by investigating narrow funnel-like interaction energy distribution. In this study, it was demonstrated that various protein interactions including kinases and E3 ubiquitin ligases have narrow funnel-like interaction energy distribution. To analyze protein interaction distribution, modified scores of iRMS and TM-score are introduced. Then, using these scores, algorithm and deep learning model for prediction of protein interaction partner and substrate of kinase and E3 ubiquitin ligase were developed. The prediction accuracy was similar to or even better than that of yeast two-hybrid screening. Ultimately, this knowledge-free protein interaction prediction method will broaden our understanding of protein interaction networks.http://www.sciencedirect.com/science/article/pii/S2589004223009884Artificial intelligenceBiochemistryBiochemistry methodsMachine learningProtein |
| spellingShingle | Juyoung Choi Narrow funnel-like interaction energy distribution is an indicator of specific protein interaction partner iScience Artificial intelligence Biochemistry Biochemistry methods Machine learning Protein |
| title | Narrow funnel-like interaction energy distribution is an indicator of specific protein interaction partner |
| title_full | Narrow funnel-like interaction energy distribution is an indicator of specific protein interaction partner |
| title_fullStr | Narrow funnel-like interaction energy distribution is an indicator of specific protein interaction partner |
| title_full_unstemmed | Narrow funnel-like interaction energy distribution is an indicator of specific protein interaction partner |
| title_short | Narrow funnel-like interaction energy distribution is an indicator of specific protein interaction partner |
| title_sort | narrow funnel like interaction energy distribution is an indicator of specific protein interaction partner |
| topic | Artificial intelligence Biochemistry Biochemistry methods Machine learning Protein |
| url | http://www.sciencedirect.com/science/article/pii/S2589004223009884 |
| work_keys_str_mv | AT juyoungchoi narrowfunnellikeinteractionenergydistributionisanindicatorofspecificproteininteractionpartner |