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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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Detalles Bibliográficos
Autor principal: Wheeler, Richard John
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
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
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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.
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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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