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IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank
We describe a server that allows the interrogation of the Protein Data Bank for hypothetical 3D side chain patterns that are not limited to known patterns from existing 3D structures. A minimal side chain description allows a variety of side chain orientations to exist within the pattern, and generi...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692123/ https://www.ncbi.nlm.nih.gov/pubmed/23716645 http://dx.doi.org/10.1093/nar/gkt431 |
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author | Nadzirin, Nurul Willett, Peter Artymiuk, Peter J. Firdaus-Raih, Mohd |
author_facet | Nadzirin, Nurul Willett, Peter Artymiuk, Peter J. Firdaus-Raih, Mohd |
author_sort | Nadzirin, Nurul |
collection | PubMed |
description | We describe a server that allows the interrogation of the Protein Data Bank for hypothetical 3D side chain patterns that are not limited to known patterns from existing 3D structures. A minimal side chain description allows a variety of side chain orientations to exist within the pattern, and generic side chain types such as acid, base and hydroxyl-containing can be additionally deployed in the search query. Moreover, only a subset of distances between the side chains need be specified. We illustrate these capabilities in case studies involving arginine stacks, serine-acid group arrangements and multiple catalytic triad-like configurations. The IMAAAGINE server can be accessed at http://mfrlab.org/grafss/imaaagine/. |
format | Online Article Text |
id | pubmed-3692123 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-36921232013-06-25 IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank Nadzirin, Nurul Willett, Peter Artymiuk, Peter J. Firdaus-Raih, Mohd Nucleic Acids Res Articles We describe a server that allows the interrogation of the Protein Data Bank for hypothetical 3D side chain patterns that are not limited to known patterns from existing 3D structures. A minimal side chain description allows a variety of side chain orientations to exist within the pattern, and generic side chain types such as acid, base and hydroxyl-containing can be additionally deployed in the search query. Moreover, only a subset of distances between the side chains need be specified. We illustrate these capabilities in case studies involving arginine stacks, serine-acid group arrangements and multiple catalytic triad-like configurations. The IMAAAGINE server can be accessed at http://mfrlab.org/grafss/imaaagine/. Oxford University Press 2013-07 2013-05-28 /pmc/articles/PMC3692123/ /pubmed/23716645 http://dx.doi.org/10.1093/nar/gkt431 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles Nadzirin, Nurul Willett, Peter Artymiuk, Peter J. Firdaus-Raih, Mohd IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank |
title | IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank |
title_full | IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank |
title_fullStr | IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank |
title_full_unstemmed | IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank |
title_short | IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank |
title_sort | imaaagine: a webserver for searching hypothetical 3d amino acid side chain arrangements in the protein data bank |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692123/ https://www.ncbi.nlm.nih.gov/pubmed/23716645 http://dx.doi.org/10.1093/nar/gkt431 |
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