Document Detail


Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps.
MedLine Citation:
PMID:  22696403     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
The complex interplay of proteins and other molecules, often in the form of large transitory assemblies, are critical to cellular function. Today, X-ray crystallography and electron cryo-microscopy (cryo-EM) are routinely used to image these macromolecular complexes, though often at limited resolutions. Despite the rapidly growing number of macromolecular structures, few tools exist for modeling and annotating structures in the range of 3-10 Å resolution. To address this need, we have developed a number of utilities specifically targeting subnanometer resolution density maps. As part of the 2010 Cryo-EM Modeling Challenge, we demonstrated two of our latest de novo modeling tools, Pathwalking and Gorgon, as well as a tool for secondary structure identification (SSEHunter) and a new rigid-body/flexible fitting tool in Gorgon. In total, we submitted 30 structural models from ten different subnanometer resolution data sets in four of the six challenge categories. Each of our utlities produced accurate structural models and annotations across the various density maps. In the end, the utilities that we present here offer users a robust toolkit for analyzing and modeling protein structure in macromolecular assemblies at non-atomic resolutions.
Authors:
Matthew L Baker; Mariah R Baker; Corey F Hryc; Tao Ju; Wah Chiu
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.    
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:  2014-01-27    
Medline Journal Info:
Nlm Unique ID:  0372525     Medline TA:  Biopolymers     Country:  United States    
Other Details:
Languages:  eng     Pagination:  655-68     Citation Subset:  IM    
Copyright Information:
Copyright © 2012 Wiley Periodicals, Inc.
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MeSH Terms
Descriptor/Qualifier:
Cryoelectron Microscopy / methods*
Models, Molecular*
Nanotechnology
Protein Structure, Secondary
Proteins / chemistry*
Grant Support
ID/Acronym/Agency:
P41 RR002250/RR/NCRR NIH HHS; P41RR002250/RR/NCRR NIH HHS; R01 GM079429/GM/NIGMS NIH HHS; R01GM079429/GM/NIGMS NIH HHS; T15LM007093/LM/NLM NIH HHS
Chemical
Reg. No./Substance:
0/Proteins
Comments/Corrections

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