%0 Journal Article
%A Wang, Z.
%A Schröder, G.F.
%T Real-space Refinement with DireX: From Global Fitting to Side-chain Improvements
%J Biopolymers
%V 97
%@ 0006-3525
%C New York, NY
%I Wiley
%M PreJuSER-111912
%P S687 - S697
%D 2012
%Z Record converted from VDB: 16.11.2012
%X 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.
%K Antigens, Viral: chemistry
%K Aquaporins: chemistry
%K Capsid Proteins: chemistry
%K Chaperonin 10: chemistry
%K Chaperonin 60: chemistry
%K Cryoelectron Microscopy: methods
%K Eye Proteins: chemistry
%K Models, Molecular
%K Proteins: chemistry
%K Software
%K Antigens, Viral (NLM Chemicals)
%K Aquaporins (NLM Chemicals)
%K Capsid Proteins (NLM Chemicals)
%K Chaperonin 10 (NLM Chemicals)
%K Chaperonin 60 (NLM Chemicals)
%K Eye Proteins (NLM Chemicals)
%K Proteins (NLM Chemicals)
%K VP6 protein, Rotavirus (NLM Chemicals)
%K aquaporin 0 (NLM Chemicals)
%K J (WoSType)
%F PUB:(DE-HGF)16
%9 Journal Article
%$ pmid:22696405
%U <Go to ISI:>//WOS:000305183000005
%R 10.1002/bip.22046
%U https://juser.fz-juelich.de/record/111912