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000111912 0247_ $$2pmid$$apmid:22696405
000111912 0247_ $$2DOI$$a10.1002/bip.22046
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000111912 041__ $$aeng
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000111912 084__ $$2WoS$$aBiochemistry & Molecular Biology
000111912 084__ $$2WoS$$aBiophysics
000111912 1001_ $$0P:(DE-Juel1)144087$$aWang, Z.$$b0$$uFZJ
000111912 245__ $$aReal-space Refinement with DireX: From Global Fitting to Side-chain Improvements
000111912 260__ $$aNew York, NY$$bWiley$$c2012
000111912 300__ $$aS687 - S697
000111912 3367_ $$0PUB:(DE-HGF)16$$2PUB:(DE-HGF)$$aJournal Article
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000111912 440_0 $$011661$$aBiopolymers$$v97$$x0006-3525$$y9
000111912 500__ $$aRecord converted from VDB: 16.11.2012
000111912 520__ $$aSingle-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.
000111912 536__ $$0G:(DE-Juel1)FUEK409$$2G:(DE-HGF)$$aFunktion und Dysfunktion des Nervensystems$$cP33$$x0
000111912 536__ $$0G:(DE-Juel1)FUEK505$$aBioSoft: Makromolekulare Systeme und biologische Informationsverarbeitung$$cP45$$x1
000111912 588__ $$aDataset connected to Web of Science, Pubmed
000111912 650_2 $$2MeSH$$aAntigens, Viral: chemistry
000111912 650_2 $$2MeSH$$aAquaporins: chemistry
000111912 650_2 $$2MeSH$$aCapsid Proteins: chemistry
000111912 650_2 $$2MeSH$$aChaperonin 10: chemistry
000111912 650_2 $$2MeSH$$aChaperonin 60: chemistry
000111912 650_2 $$2MeSH$$aCryoelectron Microscopy: methods
000111912 650_2 $$2MeSH$$aEye Proteins: chemistry
000111912 650_2 $$2MeSH$$aModels, Molecular
000111912 650_2 $$2MeSH$$aProteins: chemistry
000111912 650_2 $$2MeSH$$aSoftware
000111912 650_7 $$00$$2NLM Chemicals$$aAntigens, Viral
000111912 650_7 $$00$$2NLM Chemicals$$aAquaporins
000111912 650_7 $$00$$2NLM Chemicals$$aCapsid Proteins
000111912 650_7 $$00$$2NLM Chemicals$$aChaperonin 10
000111912 650_7 $$00$$2NLM Chemicals$$aChaperonin 60
000111912 650_7 $$00$$2NLM Chemicals$$aEye Proteins
000111912 650_7 $$00$$2NLM Chemicals$$aProteins
000111912 650_7 $$00$$2NLM Chemicals$$aVP6 protein, Rotavirus
000111912 650_7 $$00$$2NLM Chemicals$$aaquaporin 0
000111912 650_7 $$2WoSType$$aJ
000111912 65320 $$2Author$$aCryo-EM
000111912 65320 $$2Author$$aDireX
000111912 65320 $$2Author$$alow resolution
000111912 65320 $$2Author$$aflexible fitting
000111912 65320 $$2Author$$areal-space refinement
000111912 7001_ $$0P:(DE-Juel1)132018$$aSchröder, G.F.$$b1$$uFZJ
000111912 773__ $$0PERI:(DE-600)1480801-8$$0PERI:(DE-600)1480801-8$$a10.1002/bip.22046$$gVol. 97, p. S687 - S697$$pS687 - S697$$q97<S687 - S697$$tBiopolymers$$v97$$x0006-3525$$y2012
000111912 8567_ $$uhttp://dx.doi.org/10.1002/bip.22046
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000111912 9131_ $$0G:(DE-Juel1)FUEK505$$1G:(DE-HGF)POF2-450$$2G:(DE-HGF)POF2-400$$bSchlüsseltechnologien$$kP45$$lBiologische Informationsverarbeitung$$vBioSoft: Makromolekulare Systeme und biologische Informationsverarbeitung$$x1
000111912 9132_ $$0G:(DE-HGF)POF3-551$$1G:(DE-HGF)POF3-550$$2G:(DE-HGF)POF3-500$$aDE-HGF$$bKey Technologies$$lBioSoft  Fundamentals for future Technologies in the fields of Soft Matter and Life Sciences$$vFunctional Macromolecules and Complexes$$x0
000111912 9141_ $$y2012
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