Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions
Cryo-electron microscopy produces 3D density maps of molecular machines, which consist of various molecular components such as proteins and RNA. Segmentation of individual components in such maps is a challenging task, and is mostly accomplished interactively. We present an approach based on the imm...
| Main Authors: | , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
Elsevier
2015
|
| Online Access: | http://hdl.handle.net/1721.1/99224 https://orcid.org/0000-0001-7706-6954 |
| _version_ | 1826214338929623040 |
|---|---|
| author | Pintilie, Grigore D. Zhang, Junjie Goddard, Thomas D. Chiu, Wah Gossard, David C. |
| author2 | Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science |
| author_facet | Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Pintilie, Grigore D. Zhang, Junjie Goddard, Thomas D. Chiu, Wah Gossard, David C. |
| author_sort | Pintilie, Grigore D. |
| collection | MIT |
| description | Cryo-electron microscopy produces 3D density maps of molecular machines, which consist of various molecular components such as proteins and RNA. Segmentation of individual components in such maps is a challenging task, and is mostly accomplished interactively. We present an approach based on the immersive watershed method and grouping of the resulting regions using progressively smoothed maps. The method requires only three parameters: the segmentation threshold, a smoothing step size, and the number of smoothing steps. We first apply the method to maps generated from molecular structures and use a quantitative metric to measure the segmentation accuracy. The method does not attain perfect accuracy, however it produces single or small groups of regions that roughly match individual proteins or subunits. We also present two methods for fitting of structures into density maps, based on aligning the structures with single regions or small groups of regions. The first method aligns centers and principal axes, whereas the second aligns centers and then rotates the structure to find the best fit. We describe both interactive and automated ways of using these two methods. Finally, we show segmentation and fitting results for several experimentally-obtained density maps. |
| first_indexed | 2024-09-23T16:03:48Z |
| format | Article |
| id | mit-1721.1/99224 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T16:03:48Z |
| publishDate | 2015 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | mit-1721.1/992242022-09-29T17:56:02Z Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions Pintilie, Grigore D. Zhang, Junjie Goddard, Thomas D. Chiu, Wah Gossard, David C. Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology. Department of Mechanical Engineering Pintilie, Grigore D. Gossard, David C. Cryo-electron microscopy produces 3D density maps of molecular machines, which consist of various molecular components such as proteins and RNA. Segmentation of individual components in such maps is a challenging task, and is mostly accomplished interactively. We present an approach based on the immersive watershed method and grouping of the resulting regions using progressively smoothed maps. The method requires only three parameters: the segmentation threshold, a smoothing step size, and the number of smoothing steps. We first apply the method to maps generated from molecular structures and use a quantitative metric to measure the segmentation accuracy. The method does not attain perfect accuracy, however it produces single or small groups of regions that roughly match individual proteins or subunits. We also present two methods for fitting of structures into density maps, based on aligning the structures with single regions or small groups of regions. The first method aligns centers and principal axes, whereas the second aligns centers and then rotates the structure to find the best fit. We describe both interactive and automated ways of using these two methods. Finally, we show segmentation and fitting results for several experimentally-obtained density maps. National Institutes of Health (U.S.) (Grant PN2EY016525) National Institutes of Health (U.S.) (Grant R01GM079429) National Institutes of Health (U.S.) (Grant P41RR02250) National Science Foundation (U.S.) (IIS-0705644) 2015-10-13T17:26:07Z 2015-10-13T17:26:07Z 2010-03 2010-03 Article http://purl.org/eprint/type/JournalArticle 10478477 1095-8657 http://hdl.handle.net/1721.1/99224 Pintilie, Grigore D., Junjie Zhang, Thomas D. Goddard, Wah Chiu, and David C. Gossard. “Quantitative Analysis of Cryo-EM Density Map Segmentation by Watershed and Scale-Space Filtering, and Fitting of Structures by Alignment to Regions.” Journal of Structural Biology 170, no. 3 (June 2010): 427–438. https://orcid.org/0000-0001-7706-6954 en_US http://dx.doi.org/10.1016/j.jsb.2010.03.007 Journal of Structural Biology Creative Commons Attribution-Noncommercial-NoDerivatives http://creativecommons.org/licenses/by-nc-nd/4.0/ application/pdf Elsevier PMC |
| spellingShingle | Pintilie, Grigore D. Zhang, Junjie Goddard, Thomas D. Chiu, Wah Gossard, David C. Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions |
| title | Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions |
| title_full | Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions |
| title_fullStr | Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions |
| title_full_unstemmed | Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions |
| title_short | Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions |
| title_sort | quantitative analysis of cryo em density map segmentation by watershed and scale space filtering and fitting of structures by alignment to regions |
| url | http://hdl.handle.net/1721.1/99224 https://orcid.org/0000-0001-7706-6954 |
| work_keys_str_mv | AT pintiliegrigored quantitativeanalysisofcryoemdensitymapsegmentationbywatershedandscalespacefilteringandfittingofstructuresbyalignmenttoregions AT zhangjunjie quantitativeanalysisofcryoemdensitymapsegmentationbywatershedandscalespacefilteringandfittingofstructuresbyalignmenttoregions AT goddardthomasd quantitativeanalysisofcryoemdensitymapsegmentationbywatershedandscalespacefilteringandfittingofstructuresbyalignmenttoregions AT chiuwah quantitativeanalysisofcryoemdensitymapsegmentationbywatershedandscalespacefilteringandfittingofstructuresbyalignmenttoregions AT gossarddavidc quantitativeanalysisofcryoemdensitymapsegmentationbywatershedandscalespacefilteringandfittingofstructuresbyalignmenttoregions |