A generalized approach to predicting protein-protein interactions between virus and host
Abstract Background Viral infection involves a large number of protein-protein interactions (PPIs) between virus and its host. These interactions range from the initial binding of viral coat proteins to host membrane receptor to the hijacking the host transcription machinery by viral proteins. There...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2018-08-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-018-4924-2 |
| _version_ | 1811303453377429504 |
|---|---|
| author | Xiang Zhou Byungkyu Park Daesik Choi Kyungsook Han |
| author_facet | Xiang Zhou Byungkyu Park Daesik Choi Kyungsook Han |
| author_sort | Xiang Zhou |
| collection | DOAJ |
| description | Abstract Background Viral infection involves a large number of protein-protein interactions (PPIs) between virus and its host. These interactions range from the initial binding of viral coat proteins to host membrane receptor to the hijacking the host transcription machinery by viral proteins. Therefore, identifying PPIs between virus and its host helps understand the mechanism of viral infections and design antiviral drugs. Many computational methods have been developed to predict PPIs, but most of them are intended for PPIs within a species rather than PPIs across different species such as PPIs between virus and host. Results In this study, we developed a prediction model of virus-host PPIs, which is applicable to new viruses and hosts. We tested the prediction model on independent datasets of virus-host PPIs, which were not used in training the model. Despite a low sequence similarity between proteins in training datasets and target proteins in test datasets, the prediction model showed a high performance comparable to the best performance of other methods for single virus-host PPIs. Conclusions Our method will be particularly useful to find PPIs between host and new viruses for which little information is available. The program and support data are available at http://bclab.inha.ac.kr/VirusHostPPI. |
| first_indexed | 2024-04-13T07:48:23Z |
| format | Article |
| id | doaj.art-b22b3c40db8e4f93b3ec07fafdcefb41 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T07:48:23Z |
| publishDate | 2018-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-b22b3c40db8e4f93b3ec07fafdcefb412022-12-22T02:55:38ZengBMCBMC Genomics1471-21642018-08-0119S6697710.1186/s12864-018-4924-2A generalized approach to predicting protein-protein interactions between virus and hostXiang Zhou0Byungkyu Park1Daesik Choi2Kyungsook Han3Department of Computer Engineering, Inha UniversityDepartment of Computer Engineering, Inha UniversityDepartment of Computer Engineering, Inha UniversityDepartment of Computer Engineering, Inha UniversityAbstract Background Viral infection involves a large number of protein-protein interactions (PPIs) between virus and its host. These interactions range from the initial binding of viral coat proteins to host membrane receptor to the hijacking the host transcription machinery by viral proteins. Therefore, identifying PPIs between virus and its host helps understand the mechanism of viral infections and design antiviral drugs. Many computational methods have been developed to predict PPIs, but most of them are intended for PPIs within a species rather than PPIs across different species such as PPIs between virus and host. Results In this study, we developed a prediction model of virus-host PPIs, which is applicable to new viruses and hosts. We tested the prediction model on independent datasets of virus-host PPIs, which were not used in training the model. Despite a low sequence similarity between proteins in training datasets and target proteins in test datasets, the prediction model showed a high performance comparable to the best performance of other methods for single virus-host PPIs. Conclusions Our method will be particularly useful to find PPIs between host and new viruses for which little information is available. The program and support data are available at http://bclab.inha.ac.kr/VirusHostPPI.http://link.springer.com/article/10.1186/s12864-018-4924-2Virus and hostInterspecies protein-protein interactionPrediction model |
| spellingShingle | Xiang Zhou Byungkyu Park Daesik Choi Kyungsook Han A generalized approach to predicting protein-protein interactions between virus and host BMC Genomics Virus and host Interspecies protein-protein interaction Prediction model |
| title | A generalized approach to predicting protein-protein interactions between virus and host |
| title_full | A generalized approach to predicting protein-protein interactions between virus and host |
| title_fullStr | A generalized approach to predicting protein-protein interactions between virus and host |
| title_full_unstemmed | A generalized approach to predicting protein-protein interactions between virus and host |
| title_short | A generalized approach to predicting protein-protein interactions between virus and host |
| title_sort | generalized approach to predicting protein protein interactions between virus and host |
| topic | Virus and host Interspecies protein-protein interaction Prediction model |
| url | http://link.springer.com/article/10.1186/s12864-018-4924-2 |
| work_keys_str_mv | AT xiangzhou ageneralizedapproachtopredictingproteinproteininteractionsbetweenvirusandhost AT byungkyupark ageneralizedapproachtopredictingproteinproteininteractionsbetweenvirusandhost AT daesikchoi ageneralizedapproachtopredictingproteinproteininteractionsbetweenvirusandhost AT kyungsookhan ageneralizedapproachtopredictingproteinproteininteractionsbetweenvirusandhost AT xiangzhou generalizedapproachtopredictingproteinproteininteractionsbetweenvirusandhost AT byungkyupark generalizedapproachtopredictingproteinproteininteractionsbetweenvirusandhost AT daesikchoi generalizedapproachtopredictingproteinproteininteractionsbetweenvirusandhost AT kyungsookhan generalizedapproachtopredictingproteinproteininteractionsbetweenvirusandhost |