TY  - JOUR
AU  - Wang, Z.
AU  - Schröder, G.F.
TI  - Real-space Refinement with DireX: From Global Fitting to Side-chain Improvements
JO  - Biopolymers
VL  - 97
SN  - 0006-3525
CY  - New York, NY
PB  - Wiley
M1  - PreJuSER-111912
SP  - S687 - S697
PY  - 2012
N1  - Record converted from VDB: 16.11.2012
AB  - 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.
KW  - Antigens, Viral: chemistry
KW  - Aquaporins: chemistry
KW  - Capsid Proteins: chemistry
KW  - Chaperonin 10: chemistry
KW  - Chaperonin 60: chemistry
KW  - Cryoelectron Microscopy: methods
KW  - Eye Proteins: chemistry
KW  - Models, Molecular
KW  - Proteins: chemistry
KW  - Software
KW  - Antigens, Viral (NLM Chemicals)
KW  - Aquaporins (NLM Chemicals)
KW  - Capsid Proteins (NLM Chemicals)
KW  - Chaperonin 10 (NLM Chemicals)
KW  - Chaperonin 60 (NLM Chemicals)
KW  - Eye Proteins (NLM Chemicals)
KW  - Proteins (NLM Chemicals)
KW  - VP6 protein, Rotavirus (NLM Chemicals)
KW  - aquaporin 0 (NLM Chemicals)
KW  - J (WoSType)
LB  - PUB:(DE-HGF)16
C6  - pmid:22696405
UR  - <Go to ISI:>//WOS:000305183000005
DO  - DOI:10.1002/bip.22046
UR  - https://juser.fz-juelich.de/record/111912
ER  -