Cargando…

Automated model building and protein identification in cryo-EM maps

Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention. We present ModelAngelo, a machine-learning approach for automated atomic model building in cryo-EM maps. By combining information from the cryo-EM map w...

Descripción completa

Detalles Bibliográficos
Autores principales: Jamali, Kiarash, Käll, Lukas, Zhang, Rui, Brown, Alan, Kimanius, Dari, Scheres, Sjors H.W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10245678/
https://www.ncbi.nlm.nih.gov/pubmed/37292681
http://dx.doi.org/10.1101/2023.05.16.541002
_version_ 1785054907281178624
author Jamali, Kiarash
Käll, Lukas
Zhang, Rui
Brown, Alan
Kimanius, Dari
Scheres, Sjors H.W.
author_facet Jamali, Kiarash
Käll, Lukas
Zhang, Rui
Brown, Alan
Kimanius, Dari
Scheres, Sjors H.W.
author_sort Jamali, Kiarash
collection PubMed
description Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention. We present ModelAngelo, a machine-learning approach for automated atomic model building in cryo-EM maps. By combining information from the cryo-EM map with information from protein sequence and structure in a single graph neural network, ModelAngelo builds atomic models for proteins that are of similar quality as those generated by human experts. For nucleotides, ModelAngelo builds backbones with similar accuracy as humans. By using its predicted amino acid probabilities for each residue in hidden Markov model sequence searches, ModelAngelo outperforms human experts in the identification of proteins with unknown sequences. ModelAngelo will thus remove bottlenecks and increase objectivity in cryo-EM structure determination.
format Online
Article
Text
id pubmed-10245678
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Cold Spring Harbor Laboratory
record_format MEDLINE/PubMed
spelling pubmed-102456782023-06-08 Automated model building and protein identification in cryo-EM maps Jamali, Kiarash Käll, Lukas Zhang, Rui Brown, Alan Kimanius, Dari Scheres, Sjors H.W. bioRxiv Article Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention. We present ModelAngelo, a machine-learning approach for automated atomic model building in cryo-EM maps. By combining information from the cryo-EM map with information from protein sequence and structure in a single graph neural network, ModelAngelo builds atomic models for proteins that are of similar quality as those generated by human experts. For nucleotides, ModelAngelo builds backbones with similar accuracy as humans. By using its predicted amino acid probabilities for each residue in hidden Markov model sequence searches, ModelAngelo outperforms human experts in the identification of proteins with unknown sequences. ModelAngelo will thus remove bottlenecks and increase objectivity in cryo-EM structure determination. Cold Spring Harbor Laboratory 2023-10-17 /pmc/articles/PMC10245678/ /pubmed/37292681 http://dx.doi.org/10.1101/2023.05.16.541002 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Jamali, Kiarash
Käll, Lukas
Zhang, Rui
Brown, Alan
Kimanius, Dari
Scheres, Sjors H.W.
Automated model building and protein identification in cryo-EM maps
title Automated model building and protein identification in cryo-EM maps
title_full Automated model building and protein identification in cryo-EM maps
title_fullStr Automated model building and protein identification in cryo-EM maps
title_full_unstemmed Automated model building and protein identification in cryo-EM maps
title_short Automated model building and protein identification in cryo-EM maps
title_sort automated model building and protein identification in cryo-em maps
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10245678/
https://www.ncbi.nlm.nih.gov/pubmed/37292681
http://dx.doi.org/10.1101/2023.05.16.541002
work_keys_str_mv AT jamalikiarash automatedmodelbuildingandproteinidentificationincryoemmaps
AT kalllukas automatedmodelbuildingandproteinidentificationincryoemmaps
AT zhangrui automatedmodelbuildingandproteinidentificationincryoemmaps
AT brownalan automatedmodelbuildingandproteinidentificationincryoemmaps
AT kimaniusdari automatedmodelbuildingandproteinidentificationincryoemmaps
AT scheressjorshw automatedmodelbuildingandproteinidentificationincryoemmaps