Deriving protein backbone using traces extracted from density maps at medium resolutions

Kamal Al Nasr; Jing He

doi:10.1007/978-3-319-19048-8_1

Deriving protein backbone using traces extracted from density maps at medium resolutions

Kamal Al Nasr, Jing He

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

2 Scopus citations

Abstract

Electron cryomicroscopy is an experimental technique that is capable to produce three dimensional gray-scale images for protein molecules, called density maps. At medium resolution, the atomic details of the molecule cannot be visualized from density maps. However, some features of the molecule can be seen such as the locations of major secondary structures and the skeleton of the molecule. In addition, the order and direction of the detected secondary structure traces can be inferred. We introduce a method to construct the entire model of a protein directly for traces extracted from the density map. The initial results show that this method has good potential. A single model was built for each of the 12 proteins used in the test. The RMSD100 of the models is slightly improved from our previous method.

Original language	English (US)
Title of host publication	Bioinformatics Research and Applications - 11th International Symposium, ISBRA 2015, Proceedings
Editors	Ion Măndoiu, Yaohang Li, Robert Harrison
Publisher	Springer Verlag
Pages	1-11
Number of pages	11
ISBN (Print)	9783319190471
DOIs	https://doi.org/10.1007/978-3-319-19048-8_1
State	Published - 2015
Externally published	Yes
Event	11th International Symposium on Bioinformatics Research and Applications, ISBRA 2015 - Norfolk, United States Duration: Jun 7 2015 → Jun 10 2015

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	9096
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	11th International Symposium on Bioinformatics Research and Applications, ISBRA 2015
Country/Territory	United States
City	Norfolk
Period	6/7/15 → 6/10/15

Keywords

Cryo-EM
Loop modeling
Protein modeling
Skeletonization
Volume image

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-319-19048-8_1

Cite this

Nasr, K. A., & He, J. (2015). Deriving protein backbone using traces extracted from density maps at medium resolutions. In I. Măndoiu, Y. Li, & R. Harrison (Eds.), Bioinformatics Research and Applications - 11th International Symposium, ISBRA 2015, Proceedings (pp. 1-11). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9096). Springer Verlag. https://doi.org/10.1007/978-3-319-19048-8_1

Deriving protein backbone using traces extracted from density maps at medium resolutions. / Nasr, Kamal Al; He, Jing.
Bioinformatics Research and Applications - 11th International Symposium, ISBRA 2015, Proceedings. ed. / Ion Măndoiu; Yaohang Li; Robert Harrison. Springer Verlag, 2015. p. 1-11 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9096).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Nasr, KA & He, J 2015, Deriving protein backbone using traces extracted from density maps at medium resolutions. in I Măndoiu, Y Li & R Harrison (eds), Bioinformatics Research and Applications - 11th International Symposium, ISBRA 2015, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9096, Springer Verlag, pp. 1-11, 11th International Symposium on Bioinformatics Research and Applications, ISBRA 2015, Norfolk, United States, 6/7/15. https://doi.org/10.1007/978-3-319-19048-8_1

Nasr KA, He J. Deriving protein backbone using traces extracted from density maps at medium resolutions. In Măndoiu I, Li Y, Harrison R, editors, Bioinformatics Research and Applications - 11th International Symposium, ISBRA 2015, Proceedings. Springer Verlag. 2015. p. 1-11. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-319-19048-8_1

Nasr, Kamal Al ; He, Jing. / Deriving protein backbone using traces extracted from density maps at medium resolutions. Bioinformatics Research and Applications - 11th International Symposium, ISBRA 2015, Proceedings. editor / Ion Măndoiu ; Yaohang Li ; Robert Harrison. Springer Verlag, 2015. pp. 1-11 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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title = "Deriving protein backbone using traces extracted from density maps at medium resolutions",

abstract = "Electron cryomicroscopy is an experimental technique that is capable to produce three dimensional gray-scale images for protein molecules, called density maps. At medium resolution, the atomic details of the molecule cannot be visualized from density maps. However, some features of the molecule can be seen such as the locations of major secondary structures and the skeleton of the molecule. In addition, the order and direction of the detected secondary structure traces can be inferred. We introduce a method to construct the entire model of a protein directly for traces extracted from the density map. The initial results show that this method has good potential. A single model was built for each of the 12 proteins used in the test. The RMSD100 of the models is slightly improved from our previous method.",

keywords = "Cryo-EM, Loop modeling, Protein modeling, Skeletonization, Volume image",

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N2 - Electron cryomicroscopy is an experimental technique that is capable to produce three dimensional gray-scale images for protein molecules, called density maps. At medium resolution, the atomic details of the molecule cannot be visualized from density maps. However, some features of the molecule can be seen such as the locations of major secondary structures and the skeleton of the molecule. In addition, the order and direction of the detected secondary structure traces can be inferred. We introduce a method to construct the entire model of a protein directly for traces extracted from the density map. The initial results show that this method has good potential. A single model was built for each of the 12 proteins used in the test. The RMSD100 of the models is slightly improved from our previous method.

AB - Electron cryomicroscopy is an experimental technique that is capable to produce three dimensional gray-scale images for protein molecules, called density maps. At medium resolution, the atomic details of the molecule cannot be visualized from density maps. However, some features of the molecule can be seen such as the locations of major secondary structures and the skeleton of the molecule. In addition, the order and direction of the detected secondary structure traces can be inferred. We introduce a method to construct the entire model of a protein directly for traces extracted from the density map. The initial results show that this method has good potential. A single model was built for each of the 12 proteins used in the test. The RMSD100 of the models is slightly improved from our previous method.

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Deriving protein backbone using traces extracted from density maps at medium resolutions

Abstract

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Keywords

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