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A resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure
AlphaFold2 and RoseTTAfold represent a transformative advance for predicting protein structure. They are able to make very high-quality predictions given a high-quality alignment of the protein sequence with related proteins. These predictions are now readily available via the AlphaFold database of...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Public Library of Science
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8584756/ https://www.ncbi.nlm.nih.gov/pubmed/34762696 http://dx.doi.org/10.1371/journal.pone.0259871 |
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author | Wheeler, Richard John |
author_facet | Wheeler, Richard John |
author_sort | Wheeler, Richard John |
collection | PubMed |
description | AlphaFold2 and RoseTTAfold represent a transformative advance for predicting protein structure. They are able to make very high-quality predictions given a high-quality alignment of the protein sequence with related proteins. These predictions are now readily available via the AlphaFold database of predicted structures and AlphaFold or RoseTTAfold Colaboratory notebooks for custom predictions. However, predictions for some species tend to be lower confidence than model organisms. Problematic species include Trypanosoma cruzi and Leishmania infantum: important unicellular eukaryotic human parasites in an early-branching eukaryotic lineage. The cause appears to be due to poor sampling of this branch of life (Discoba) in the protein sequences databases used for the AlphaFold database and ColabFold. Here, by comprehensively gathering openly available protein sequence data for Discoba species, significant improvements to AlphaFold2 protein structure prediction over the AlphaFold database and ColabFold are demonstrated. This is made available as an easy-to-use tool for the parasitology community in the form of Colaboratory notebooks for generating multiple sequence alignments and AlphaFold2 predictions of protein structure for Trypanosoma, Leishmania and related species. |
format | Online Article Text |
id | pubmed-8584756 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-85847562021-11-12 A resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure Wheeler, Richard John PLoS One Research Article AlphaFold2 and RoseTTAfold represent a transformative advance for predicting protein structure. They are able to make very high-quality predictions given a high-quality alignment of the protein sequence with related proteins. These predictions are now readily available via the AlphaFold database of predicted structures and AlphaFold or RoseTTAfold Colaboratory notebooks for custom predictions. However, predictions for some species tend to be lower confidence than model organisms. Problematic species include Trypanosoma cruzi and Leishmania infantum: important unicellular eukaryotic human parasites in an early-branching eukaryotic lineage. The cause appears to be due to poor sampling of this branch of life (Discoba) in the protein sequences databases used for the AlphaFold database and ColabFold. Here, by comprehensively gathering openly available protein sequence data for Discoba species, significant improvements to AlphaFold2 protein structure prediction over the AlphaFold database and ColabFold are demonstrated. This is made available as an easy-to-use tool for the parasitology community in the form of Colaboratory notebooks for generating multiple sequence alignments and AlphaFold2 predictions of protein structure for Trypanosoma, Leishmania and related species. Public Library of Science 2021-11-11 /pmc/articles/PMC8584756/ /pubmed/34762696 http://dx.doi.org/10.1371/journal.pone.0259871 Text en © 2021 Richard John Wheeler https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Wheeler, Richard John A resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure |
title | A resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure |
title_full | A resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure |
title_fullStr | A resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure |
title_full_unstemmed | A resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure |
title_short | A resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure |
title_sort | resource for improved predictions of trypanosoma and leishmania protein three-dimensional structure |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8584756/ https://www.ncbi.nlm.nih.gov/pubmed/34762696 http://dx.doi.org/10.1371/journal.pone.0259871 |
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