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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Autor principal:	Richard John Wheeler
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/83b2109ced794341949d3298902a88ba
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id	oai:doaj.org-article:83b2109ced794341949d3298902a88ba
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spelling	oai:doaj.org-article:83b2109ced794341949d3298902a88ba2021-12-02T20:07:35ZA resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure.1932-620310.1371/journal.pone.0259871https://doaj.org/article/83b2109ced794341949d3298902a88ba2021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0259871https://doaj.org/toc/1932-6203AlphaFold2 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.Richard John WheelerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 11, p e0259871 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Richard John Wheeler A resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure.
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	article
author	Richard John Wheeler
author_facet	Richard John Wheeler
author_sort	Richard John Wheeler
title	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_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_sort	resource for improved predictions of trypanosoma and leishmania protein three-dimensional structure.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/83b2109ced794341949d3298902a88ba
work_keys_str_mv	AT richardjohnwheeler aresourceforimprovedpredictionsoftrypanosomaandleishmaniaproteinthreedimensionalstructure AT richardjohnwheeler resourceforimprovedpredictionsoftrypanosomaandleishmaniaproteinthreedimensionalstructure
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A resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure.

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