Jupytope: computational extraction of structural properties of viral epitopes
Epitope residues located on viral surface proteins are of immense interest in immunology and related applications such as vaccine development, disease diagnosis and drug design. Most tools rely on sequence-based statistical comparisons, such as information entropy of residue positions in aligned col...
| Autors principals: | , , |
|---|---|
| Altres autors: | |
| Format: | Journal Article |
| Idioma: | English |
| Publicat: |
2024
|
| Matèries: | |
| Accés en línia: | https://hdl.handle.net/10356/178480 |
| _version_ | 1826111752844083200 |
|---|---|
| author | Rashid, Shamima Ng, Teng Ann Kwoh, Chee Keong |
| author2 | School of Computer Science and Engineering |
| author_facet | School of Computer Science and Engineering Rashid, Shamima Ng, Teng Ann Kwoh, Chee Keong |
| author_sort | Rashid, Shamima |
| collection | NTU |
| description | Epitope residues located on viral surface proteins are of immense interest in immunology and related applications such as vaccine development, disease diagnosis and drug design. Most tools rely on sequence-based statistical comparisons, such as information entropy of residue positions in aligned columns to infer location and properties of epitope sites. To facilitate cross-structural comparisons of epitopes on viral surface proteins, a python-based extraction tool implemented with Jupyter notebook is presented (Jupytope). Given a viral antigen structure of interest, a list of known epitope sites and a reference structure, the corresponding epitope structural properties can quickly be obtained. The tool integrates biopython modules for commonly used software such as NACCESS, DSSP as well as residue depth and outputs a list of structure-derived properties such as dihedral angles, solvent accessibility, residue depth and secondary structure that can be saved in several convenient data formats. To ensure correct spatial alignment, Jupytope takes a list of given epitope sites and their corresponding reference structure and aligns them before extracting the desired properties. Examples are demonstrated for epitopes of Influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) viral strains. The extracted properties assist detection of two Influenza subtypes and show potential in distinguishing between four major clades of SARS-CoV2, as compared with randomized labels. The tool will facilitate analytical and predictive works on viral epitopes through the extracted structural information. Jupytope and extracted datasets are available at https://github.com/shamimarashid/Jupytope. |
| first_indexed | 2024-10-01T02:55:59Z |
| format | Journal Article |
| id | ntu-10356/178480 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T02:55:59Z |
| publishDate | 2024 |
| record_format | dspace |
| spelling | ntu-10356/1784802024-06-28T15:35:41Z Jupytope: computational extraction of structural properties of viral epitopes Rashid, Shamima Ng, Teng Ann Kwoh, Chee Keong School of Computer Science and Engineering Biomedical Informatics Lab Computer and Information Science Structure-derived properties Epitopes Epitope residues located on viral surface proteins are of immense interest in immunology and related applications such as vaccine development, disease diagnosis and drug design. Most tools rely on sequence-based statistical comparisons, such as information entropy of residue positions in aligned columns to infer location and properties of epitope sites. To facilitate cross-structural comparisons of epitopes on viral surface proteins, a python-based extraction tool implemented with Jupyter notebook is presented (Jupytope). Given a viral antigen structure of interest, a list of known epitope sites and a reference structure, the corresponding epitope structural properties can quickly be obtained. The tool integrates biopython modules for commonly used software such as NACCESS, DSSP as well as residue depth and outputs a list of structure-derived properties such as dihedral angles, solvent accessibility, residue depth and secondary structure that can be saved in several convenient data formats. To ensure correct spatial alignment, Jupytope takes a list of given epitope sites and their corresponding reference structure and aligns them before extracting the desired properties. Examples are demonstrated for epitopes of Influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) viral strains. The extracted properties assist detection of two Influenza subtypes and show potential in distinguishing between four major clades of SARS-CoV2, as compared with randomized labels. The tool will facilitate analytical and predictive works on viral epitopes through the extracted structural information. Jupytope and extracted datasets are available at https://github.com/shamimarashid/Jupytope. Ministry of Education (MOE) Published version This work was funded by Ministry of Education (MOE) grants MOE2019-T2-2-175 and MOE2020-T1-001-130, Singapore. 2024-06-24T01:51:23Z 2024-06-24T01:51:23Z 2022 Journal Article Rashid, S., Ng, T. A. & Kwoh, C. K. (2022). Jupytope: computational extraction of structural properties of viral epitopes. Briefings in Bioinformatics, 23(6), 1-13. https://dx.doi.org/10.1093/bib/bbac362 1467-5463 https://hdl.handle.net/10356/178480 10.1093/bib/bbac362 36094101 2-s2.0-85142403482 6 23 1 13 en MOE2019-T2-2-175 MOE2020-T1-001-130 Briefings in Bioinformatics © The Author(s) 2022. Published by Oxford University Press. All rights reserved. This article may be downloaded for personal use only. Any other use requires prior permission of the copyright holder. The Version of Record is available online at http://doi.org/10.1093/bib/bbac362 application/pdf |
| spellingShingle | Computer and Information Science Structure-derived properties Epitopes Rashid, Shamima Ng, Teng Ann Kwoh, Chee Keong Jupytope: computational extraction of structural properties of viral epitopes |
| title | Jupytope: computational extraction of structural properties of viral epitopes |
| title_full | Jupytope: computational extraction of structural properties of viral epitopes |
| title_fullStr | Jupytope: computational extraction of structural properties of viral epitopes |
| title_full_unstemmed | Jupytope: computational extraction of structural properties of viral epitopes |
| title_short | Jupytope: computational extraction of structural properties of viral epitopes |
| title_sort | jupytope computational extraction of structural properties of viral epitopes |
| topic | Computer and Information Science Structure-derived properties Epitopes |
| url | https://hdl.handle.net/10356/178480 |
| work_keys_str_mv | AT rashidshamima jupytopecomputationalextractionofstructuralpropertiesofviralepitopes AT ngtengann jupytopecomputationalextractionofstructuralpropertiesofviralepitopes AT kwohcheekeong jupytopecomputationalextractionofstructuralpropertiesofviralepitopes |