Fast and automated protein-DNA/RNA macromolecular complex modeling from cryo-EM maps
Abstract Cryo-electron microscopy (cryo-EM) allows a macromolecular structure such as protein-DNA/RNA complexes to be reconstructed in a three-dimensional coulomb potential map. The structural information of these macromolecular complexes forms the foundation for understanding the molecular mechanis...
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Published in | Briefings in bioinformatics Vol. 24; no. 2 |
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Main Authors | , , , , , , |
Format | Journal Article |
Language | English |
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England
Oxford University Press
19.03.2023
Oxford Publishing Limited (England) |
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Abstract | Abstract
Cryo-electron microscopy (cryo-EM) allows a macromolecular structure such as protein-DNA/RNA complexes to be reconstructed in a three-dimensional coulomb potential map. The structural information of these macromolecular complexes forms the foundation for understanding the molecular mechanism including many human diseases. However, the model building of large macromolecular complexes is often difficult and time-consuming. We recently developed DeepTracer-2.0, an artificial-intelligence-based pipeline that can build amino acid and nucleic acid backbones from a single cryo-EM map, and even predict the best-fitting residues according to the density of side chains. The experiments showed improved accuracy and efficiency when benchmarking the performance on independent experimental maps of protein-DNA/RNA complexes and demonstrated the promising future of macromolecular modeling from cryo-EM maps. Our method and pipeline could benefit researchers worldwide who work in molecular biomedicine and drug discovery, and substantially increase the throughput of the cryo-EM model building. The pipeline has been integrated into the web portal https://deeptracer.uw.edu/. |
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AbstractList | Abstract
Cryo-electron microscopy (cryo-EM) allows a macromolecular structure such as protein-DNA/RNA complexes to be reconstructed in a three-dimensional coulomb potential map. The structural information of these macromolecular complexes forms the foundation for understanding the molecular mechanism including many human diseases. However, the model building of large macromolecular complexes is often difficult and time-consuming. We recently developed DeepTracer-2.0, an artificial-intelligence-based pipeline that can build amino acid and nucleic acid backbones from a single cryo-EM map, and even predict the best-fitting residues according to the density of side chains. The experiments showed improved accuracy and efficiency when benchmarking the performance on independent experimental maps of protein-DNA/RNA complexes and demonstrated the promising future of macromolecular modeling from cryo-EM maps. Our method and pipeline could benefit researchers worldwide who work in molecular biomedicine and drug discovery, and substantially increase the throughput of the cryo-EM model building. The pipeline has been integrated into the web portal https://deeptracer.uw.edu/. Cryo-electron microscopy (cryo-EM) allows a macromolecular structure such as protein-DNA/RNA complexes to be reconstructed in a three-dimensional coulomb potential map. The structural information of these macromolecular complexes forms the foundation for understanding the molecular mechanism including many human diseases. However, the model building of large macromolecular complexes is often difficult and time-consuming. We recently developed DeepTracer-2.0, an artificial-intelligence-based pipeline that can build amino acid and nucleic acid backbones from a single cryo-EM map, and even predict the best-fitting residues according to the density of side chains. The experiments showed improved accuracy and efficiency when benchmarking the performance on independent experimental maps of protein-DNA/RNA complexes and demonstrated the promising future of macromolecular modeling from cryo-EM maps. Our method and pipeline could benefit researchers worldwide who work in molecular biomedicine and drug discovery, and substantially increase the throughput of the cryo-EM model building. The pipeline has been integrated into the web portal https://deeptracer.uw.edu/. Cryo-electron microscopy (cryo-EM) allows a macromolecular structure such as protein-DNA/RNA complexes to be reconstructed in a three-dimensional coulomb potential map. The structural information of these macromolecular complexes forms the foundation for understanding the molecular mechanism including many human diseases. However, the model building of large macromolecular complexes is often difficult and time-consuming. We recently developed DeepTracer-2.0, an artificial-intelligence-based pipeline that can build amino acid and nucleic acid backbones from a single cryo-EM map, and even predict the best-fitting residues according to the density of side chains. The experiments showed improved accuracy and efficiency when benchmarking the performance on independent experimental maps of protein-DNA/RNA complexes and demonstrated the promising future of macromolecular modeling from cryo-EM maps. Our method and pipeline could benefit researchers worldwide who work in molecular biomedicine and drug discovery, and substantially increase the throughput of the cryo-EM model building. The pipeline has been integrated into the web portal https://deeptracer.uw.edu/ . |
Author | Cao, Renzhi Zhao, Minglei Wang, Fengbin Si, Dong Nakamura, Andrew Meng, Hanze Hou, Jie |
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Cites_doi | 10.1002/jcc.25802 10.1126/science.abl4546 10.1073/pnas.2017525118 10.1038/s41592-020-01051-w 10.1107/S2059798319011471 10.1038/s41467-021-22577-3 10.1007/s10822-014-9770-y 10.1038/s41592-021-01389-9 10.1107/S1399004715000383 10.1093/nar/gkv1126 10.1073/pnas.2108859118 10.1107/S0108767310039140 10.1016/j.str.2012.01.023 10.1089/cmb.2014.0156 10.1002/anie.202000421 10.1038/s41592-018-0173-1 10.1109/BIBM.2018.8621288 10.1038/s41592-019-0500-1 10.1093/nar/28.1.235 10.1016/j.jsb.2019.107416 10.1016/j.cell.2017.06.050 10.1038/s41467-018-04053-7 |
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Keywords | protein-DNA/RNA macromolecular modeling machine learning cryo-EM artificial intelligence |
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Cryo-electron microscopy (cryo-EM) allows a macromolecular structure such as protein-DNA/RNA complexes to be reconstructed in a three-dimensional... Cryo-electron microscopy (cryo-EM) allows a macromolecular structure such as protein-DNA/RNA complexes to be reconstructed in a three-dimensional coulomb... |
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SubjectTerms | Amino acids Coulomb potential Cryoelectron Microscopy - methods Deoxyribonucleic acid DNA DNA structure Electron microscopy Human diseases Humans Macromolecular Substances - chemistry Macromolecules Modelling Models, Molecular Molecular modelling Molecular structure Nucleic acids Problem Solving Protocol Protein Conformation Protein structure Proteins Ribonucleic acid RNA |
Title | Fast and automated protein-DNA/RNA macromolecular complex modeling from cryo-EM maps |
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