Document Detail


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
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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:  2013-09-03    
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.
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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
Comments/Corrections

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