Document Detail


Real-space refinement with DireX: From global fitting to side-chain improvements.
MedLine Citation:
PMID:  22696405     Owner:  NLM     Status:  In-Data-Review    
Abstract/OtherAbstract:
Single-particle cryo-electron microscopy (cryo-EM) has become an important tool to determine the structure of large biomolecules and assemblies thereof. However, the achievable resolution varies considerably over a wide range of about 3.5-20 Å. The interpretation of these intermediate- to low-resolution density maps in terms of atomic models is a big challenge and an area of active research. Here, we present our real-space structure refinement program DireX, which was developed primarily for cryo-EM-derived density maps. The basic principle and its main features are described. DireX employs Deformable Elastic Network (DEN) restraints to reduce overfitting by decreasing the effective number of degrees of freedom used in the refinement. Missing or reduced density due to flexible parts of the protein can lead to artifacts in the structure refinement, which is addressed through the concept of restrained grouped occupancy refinement. Furthermore, we describe the performance of DireX in the 2010 Cryo-EM Modeling Challenge, where we chose six density maps of four different proteins provided by the Modeling Challenge exemplifying typical refinement results at a large resolution range from 3 to 23 Å. © 2012 Wiley Periodicals, Inc. Biopolymers 97: 687-697, 2012.
Authors:
Zhe Wang; Gunnar F Schröder
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Publication Detail:
Type:  Journal Article    
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:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  0372525     Medline TA:  Biopolymers     Country:  United States    
Other Details:
Languages:  eng     Pagination:  687-97     Citation Subset:  IM    
Copyright Information:
Copyright © 2012 Wiley Periodicals, Inc.
Affiliation:
Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
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