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/f5af0dacc2144a69be1c1bdc391e80c7
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id	oai:doaj.org-article:f5af0dacc2144a69be1c1bdc391e80c7
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spelling	oai:doaj.org-article:f5af0dacc2144a69be1c1bdc391e80c72021-11-18T08:14:34ZA resource for improved predictions of Trypanosoma and Leishmania protein three-dimensional structure1932-6203https://doaj.org/article/f5af0dacc2144a69be1c1bdc391e80c72021-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8584756/?tool=EBIhttps://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 (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/f5af0dacc2144a69be1c1bdc391e80c7
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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