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IRAM: virus capsid database and analysis resource
IRAM is an online, open access, comprehensive database and analysis resource for virus capsids. The database includes over 200 000 hierarchically organized capsid-associated nucleotide and amino acid sequences, as well as 193 capsids structures of high resolution (1–5 Å). Each capsid’s structure inc...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6637973/ https://www.ncbi.nlm.nih.gov/pubmed/31318422 http://dx.doi.org/10.1093/database/baz079 |
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author | Almansour, Iman Alhagri, Mazen Alfares, Rahaf Alshehri, Manal Bakhashwain, Razan Maarouf, Ahmed |
author_facet | Almansour, Iman Alhagri, Mazen Alfares, Rahaf Alshehri, Manal Bakhashwain, Razan Maarouf, Ahmed |
author_sort | Almansour, Iman |
collection | PubMed |
description | IRAM is an online, open access, comprehensive database and analysis resource for virus capsids. The database includes over 200 000 hierarchically organized capsid-associated nucleotide and amino acid sequences, as well as 193 capsids structures of high resolution (1–5 Å). Each capsid’s structure includes a data file for capsid domain (PDB), capsid symmetry unit (PDB) and capsid structure information (PSF); these contain capsid structural information that is necessary to run further computational studies. Physicochemical properties analysis is implemented for calculating capsid total charge at given radii and for calculating charge distributions. This resource includes BLASTn and BLASTp tools, which can be applied to compare nucleotide and amino acid sequences. The diverse functionality of IRAM is valuable to researchers because it integrates different aspects of virus capsids via a user-friendly interface. Such data are critical for studying capsid evolution and patterns of conservation. The IRAM database can also provide initial necessary information for the design of synthetic capsids for various biotechnological applications. |
format | Online Article Text |
id | pubmed-6637973 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-66379732019-07-22 IRAM: virus capsid database and analysis resource Almansour, Iman Alhagri, Mazen Alfares, Rahaf Alshehri, Manal Bakhashwain, Razan Maarouf, Ahmed Database (Oxford) Original Article IRAM is an online, open access, comprehensive database and analysis resource for virus capsids. The database includes over 200 000 hierarchically organized capsid-associated nucleotide and amino acid sequences, as well as 193 capsids structures of high resolution (1–5 Å). Each capsid’s structure includes a data file for capsid domain (PDB), capsid symmetry unit (PDB) and capsid structure information (PSF); these contain capsid structural information that is necessary to run further computational studies. Physicochemical properties analysis is implemented for calculating capsid total charge at given radii and for calculating charge distributions. This resource includes BLASTn and BLASTp tools, which can be applied to compare nucleotide and amino acid sequences. The diverse functionality of IRAM is valuable to researchers because it integrates different aspects of virus capsids via a user-friendly interface. Such data are critical for studying capsid evolution and patterns of conservation. The IRAM database can also provide initial necessary information for the design of synthetic capsids for various biotechnological applications. Oxford University Press 2019-07-18 /pmc/articles/PMC6637973/ /pubmed/31318422 http://dx.doi.org/10.1093/database/baz079 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Article Almansour, Iman Alhagri, Mazen Alfares, Rahaf Alshehri, Manal Bakhashwain, Razan Maarouf, Ahmed IRAM: virus capsid database and analysis resource |
title | IRAM: virus capsid database and analysis resource |
title_full | IRAM: virus capsid database and analysis resource |
title_fullStr | IRAM: virus capsid database and analysis resource |
title_full_unstemmed | IRAM: virus capsid database and analysis resource |
title_short | IRAM: virus capsid database and analysis resource |
title_sort | iram: virus capsid database and analysis resource |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6637973/ https://www.ncbi.nlm.nih.gov/pubmed/31318422 http://dx.doi.org/10.1093/database/baz079 |
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