| Macromolecular structure modeling from 3D EM using VolRover 2.0. | |
| | |
MedLine Citation:
|
PMID: 22696407 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
|
We review tools for structure identification and model-based refinement from three-dimensional electron microscopy implemented in our in-house software package, VOLROVER 2.0. For viral density maps with icosahedral symmetry, we segment the capsid, polymeric, and monomeric subunits using techniques based on automatic symmetry detection and multidomain fast marching. For large biomolecules without symmetry information, we again use our multidomain fast-marching method with manual or fit-based multiseeding to segment meaningful substructures. In either case, we subject the resulting segmented subunit to secondary structure detection when the EM resolution is sufficiently high, and rigid-body structure fitting when the corresponding X-ray structure is available. Secondary structure elements are identified by three techniques: our earlier volume-based and boundary-based skeletonization methods as well as a new method, currently in development, based on solving the grassfire flow equation. For rigid-body fitting, we adapt our earlier fast Fourier-based correlation scheme F2Dock. Our reported segmentation, secondary structure elements identification, and rigid-body fitting techniques, implemented in VOLROVER 2.0 are applied to the PSB 2011 cryo-EM modeling challenge data, and our results are briefly compared to similar results submitted from other research groups. The comparisons show that our techniques are equally capable of segmenting relatively accurate subunits from a viral or protein assembly, and that high segmentation quality leads in turn to higher-quality results of secondary structure elements identification and correlation-based rigid-body fitting. © 2012 Wiley Periodicals, Inc. Biopolymers 97: 709-731, 2012. |
| | |
Authors:
|
Qin Zhang; Radhakrishna Bettadapura; Chandrajit Bajaj |
Related Documents
:
|
22809307 - Neural system modeling and simulation using hybrid functional petri net. 23431377 - Structural properties and complexity of a new network class: collatz step graphs. 22391487 - Multiplexing and multivariate analysis in neurodegeneration. 23456507 - Can an engineer fix an immune system?-rethinking theoretical biology. 8776917 - Megatrials are based on a methodological mistake. 16850767 - Interpretation of bootstrap values in phylogenetic analysis. |
Publication Detail:
|
Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Review |
Journal Detail:
|
Title: Biopolymers Volume: 97 ISSN: 0006-3525 ISO Abbreviation: Biopolymers Publication Date: 2012 Sep |
Date Detail:
|
Created Date: 2012-06-14 Completed Date: 2012-08-21 Revised Date: 2013-04-16 |
Medline Journal Info:
|
Nlm Unique ID: 0372525 Medline TA: Biopolymers Country: United States |
Other Details:
|
Languages: eng Pagination: 709-31 Citation Subset: IM |
Copyright Information:
|
Copyright © 2012 Wiley Periodicals, Inc. |
Affiliation:
|
Institute for Computational Engineering and Sciences, The University of Texas, Austin, TX 78712, USA. |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
Chaperonin 10
/
chemistry Chaperonin 60 / chemistry Cryoelectron Microscopy / methods* Models, Molecular* Protein Structure, Secondary Proteins / chemistry* Ribosomes / ultrastructure Software* |
| Grant Support | |
ID/Acronym/Agency:
|
R01 EB004873/EB/NIBIB NIH HHS; R01 EB004873-04/EB/NIBIB NIH HHS; R01 GM074258/GM/NIGMS NIH HHS; R01 GM074258-03S1/GM/NIGMS NIH HHS; R01-EB004873/EB/NIBIB NIH HHS |
| Chemical | |
Reg. No./Substance:
|
0/Chaperonin 10; 0/Chaperonin 60; 0/Proteins |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: A machine learning approach for the identification of protein secondary structure elements from elec...
Next Document: Nhs: network-based hierarchical segmentation for cryo-electron microscopy density maps.