NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interface
Abstract Background Vaccines development in this millennium started by the milestone work on Neisseria meningitidis B, reporting the invention of Reverse Vaccinology (RV), which allows to identify vaccine candidates (VCs) by screening bacterial pathogens genome or proteome through computational anal...
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BMC
2024-12-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-024-06004-0 |
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| author | Andrea Conte Nicola Gulmini Francesco Costa Matteo Cartura Felix Bröhl Francesco Patanè Francesco Filippini |
| author_facet | Andrea Conte Nicola Gulmini Francesco Costa Matteo Cartura Felix Bröhl Francesco Patanè Francesco Filippini |
| author_sort | Andrea Conte |
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| description | Abstract Background Vaccines development in this millennium started by the milestone work on Neisseria meningitidis B, reporting the invention of Reverse Vaccinology (RV), which allows to identify vaccine candidates (VCs) by screening bacterial pathogens genome or proteome through computational analyses. When NERVE (New Enhanced RV Environment), the first RV software integrating tools to perform the selection of VCs, was released, it prompted further development in the field. However, the problem-solving potential of most, if not all, RV programs is still largely unexploited by experimental vaccinologists that impaired by somehow difficult interfaces, requiring bioinformatic skills. Results We report here on the development and release of NERVE 2.0 (available at: https://nerve-bio.org ) which keeps the original integrative and modular approach of NERVE, while showing higher predictive performance than its previous version and other web-RV programs (Vaxign and Vaxijen). We renewed some of its modules and added innovative ones, such as Loop-Razor, to recover fragments of promising vaccine candidates or Epitope Prediction for the epitope prediction binding affinities and population coverage. Along with two newly built AI (Artificial Intelligence)-based models: ESPAAN and Virulent. To improve user-friendliness, NERVE was shifted to a tutored, web-based interface, with a noSQL-database to consent the user to submit, obtain and retrieve analysis results at any moment. Conclusions With its redesigned and updated environment, NERVE 2.0 allows customisable and refinable bacterial protein vaccine analyses to all different kinds of users. |
| format | Article |
| id | doaj-art-e0c205cc7c7c4903b27e1df7a00d77dc |
| institution | Kabale University |
| issn | 1471-2105 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-e0c205cc7c7c4903b27e1df7a00d77dc2025-01-26T12:54:51ZengBMCBMC Bioinformatics1471-21052024-12-0125112010.1186/s12859-024-06004-0NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interfaceAndrea Conte0Nicola Gulmini1Francesco Costa2Matteo Cartura3Felix Bröhl4Francesco Patanè5Francesco Filippini6Synthetic Biology and Biotechnology Unit, Department of Biology, University of PaduaSynthetic Biology and Biotechnology Unit, Department of Biology, University of PaduaSynthetic Biology and Biotechnology Unit, Department of Biology, University of PaduaSynthetic Biology and Biotechnology Unit, Department of Biology, University of PaduaBröhl Software DevelopmentSynthetic Biology and Biotechnology Unit, Department of Biology, University of PaduaSynthetic Biology and Biotechnology Unit, Department of Biology, University of PaduaAbstract Background Vaccines development in this millennium started by the milestone work on Neisseria meningitidis B, reporting the invention of Reverse Vaccinology (RV), which allows to identify vaccine candidates (VCs) by screening bacterial pathogens genome or proteome through computational analyses. When NERVE (New Enhanced RV Environment), the first RV software integrating tools to perform the selection of VCs, was released, it prompted further development in the field. However, the problem-solving potential of most, if not all, RV programs is still largely unexploited by experimental vaccinologists that impaired by somehow difficult interfaces, requiring bioinformatic skills. Results We report here on the development and release of NERVE 2.0 (available at: https://nerve-bio.org ) which keeps the original integrative and modular approach of NERVE, while showing higher predictive performance than its previous version and other web-RV programs (Vaxign and Vaxijen). We renewed some of its modules and added innovative ones, such as Loop-Razor, to recover fragments of promising vaccine candidates or Epitope Prediction for the epitope prediction binding affinities and population coverage. Along with two newly built AI (Artificial Intelligence)-based models: ESPAAN and Virulent. To improve user-friendliness, NERVE was shifted to a tutored, web-based interface, with a noSQL-database to consent the user to submit, obtain and retrieve analysis results at any moment. Conclusions With its redesigned and updated environment, NERVE 2.0 allows customisable and refinable bacterial protein vaccine analyses to all different kinds of users.https://doi.org/10.1186/s12859-024-06004-0Reverse vaccinologyVaccine candidatesModular softwareUser-friendly websiteMachine learningArtificial intelligence |
| spellingShingle | Andrea Conte Nicola Gulmini Francesco Costa Matteo Cartura Felix Bröhl Francesco Patanè Francesco Filippini NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interface BMC Bioinformatics Reverse vaccinology Vaccine candidates Modular software User-friendly website Machine learning Artificial intelligence |
| title | NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interface |
| title_full | NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interface |
| title_fullStr | NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interface |
| title_full_unstemmed | NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interface |
| title_short | NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interface |
| title_sort | nerve 2 0 boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user friendly web interface |
| topic | Reverse vaccinology Vaccine candidates Modular software User-friendly website Machine learning Artificial intelligence |
| url | https://doi.org/10.1186/s12859-024-06004-0 |
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