DEMO-EM2 : assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting
© The Author(s) 2024. Published by Oxford University Press..
The breakthrough in cryo-electron microscopy (cryo-EM) technology has led to an increasing number of density maps of biological macromolecules. However, constructing accurate protein complex atomic structures from cryo-EM maps remains a challenge. In this study, we extend our previously developed DEMO-EM to present DEMO-EM2, an automated method for constructing protein complex models from cryo-EM maps through an iterative assembly procedure intertwining chain- and domain-level matching and fitting for predicted chain models. The method was carefully evaluated on 27 cryo-electron tomography (cryo-ET) maps and 16 single-particle EM maps, where DEMO-EM2 models achieved an average TM-score of 0.92, outperforming those of state-of-the-art methods. The results demonstrate an efficient method that enables the rapid and reliable solution of challenging cryo-EM structure modeling problems.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2024 |
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| Erschienen: |
2024 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:25 |
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| Enthalten in: |
Briefings in bioinformatics - 25(2024), 2 vom: 22. Jan. |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Zhang, Ziying [VerfasserIn] |
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| Links: |
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| Themen: |
Cryo-EM |
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| Anmerkungen: |
Date Completed 25.03.2024 Date Revised 25.03.2024 published: Print Citation Status MEDLINE |
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| doi: |
10.1093/bib/bbae113 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| 520 | |a © The Author(s) 2024. Published by Oxford University Press. | ||
| 520 | |a The breakthrough in cryo-electron microscopy (cryo-EM) technology has led to an increasing number of density maps of biological macromolecules. However, constructing accurate protein complex atomic structures from cryo-EM maps remains a challenge. In this study, we extend our previously developed DEMO-EM to present DEMO-EM2, an automated method for constructing protein complex models from cryo-EM maps through an iterative assembly procedure intertwining chain- and domain-level matching and fitting for predicted chain models. The method was carefully evaluated on 27 cryo-electron tomography (cryo-ET) maps and 16 single-particle EM maps, where DEMO-EM2 models achieved an average TM-score of 0.92, outperforming those of state-of-the-art methods. The results demonstrate an efficient method that enables the rapid and reliable solution of challenging cryo-EM structure modeling problems | ||
| 650 | 4 | |a Journal Article | |
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| 650 | 4 | |a protein structure prediction | |
| 700 | 1 | |a Cai, Yaxian |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Biao |e verfasserin |4 aut | |
| 700 | 1 | |a Zheng, Wei |e verfasserin |4 aut | |
| 700 | 1 | |a Freddolino, Lydia |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Guijun |e verfasserin |4 aut | |
| 700 | 1 | |a Zhou, Xiaogen |e verfasserin |4 aut | |
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