Hauptseite > Publikationsdatenbank > Real-space Refinement with DireX: From Global Fitting to Side-chain Improvements > print

001     111912
005     20200402205949.0
024 7 _ |2 pmid
|a pmid:22696405
024 7 _ |2 DOI
|a 10.1002/bip.22046
024 7 _ |2 WOS
|a WOS:000305183000005
024 7 _ |2 ISSN
|a 0006-3525
037 _ _ |a PreJuSER-111912
041 _ _ |a eng
082 _ _ |a 570
084 _ _ |2 WoS
|a Biochemistry & Molecular Biology
084 _ _ |2 WoS
|a Biophysics
100 1 _ |a Wang, Z.
|b 0
|u FZJ
|0 P:(DE-Juel1)144087
245 _ _ |a Real-space Refinement with DireX: From Global Fitting to Side-chain Improvements
260 _ _ |c 2012
|a New York, NY
|b Wiley
300 _ _ |a S687 - S697
336 7 _ |a Journal Article
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336 7 _ |a article
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440 _ 0 |a Biopolymers
|x 0006-3525
|0 11661
|y 9
|v 97
500 _ _ |a Record converted from VDB: 16.11.2012
520 _ _ |a 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.
536 _ _ |a Funktion und Dysfunktion des Nervensystems
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536 _ _ |a BioSoft: Makromolekulare Systeme und biologische Informationsverarbeitung
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588 _ _ |a Dataset connected to Web of Science, Pubmed
650 _ 2 |2 MeSH
|a Antigens, Viral: chemistry
650 _ 2 |2 MeSH
|a Aquaporins: chemistry
650 _ 2 |2 MeSH
|a Capsid Proteins: chemistry
650 _ 2 |2 MeSH
|a Chaperonin 10: chemistry
650 _ 2 |2 MeSH
|a Chaperonin 60: chemistry
650 _ 2 |2 MeSH
|a Cryoelectron Microscopy: methods
650 _ 2 |2 MeSH
|a Eye Proteins: chemistry
650 _ 2 |2 MeSH
|a Models, Molecular
650 _ 2 |2 MeSH
|a Proteins: chemistry
650 _ 2 |2 MeSH
|a Software
650 _ 7 |0 0
|2 NLM Chemicals
|a Antigens, Viral
650 _ 7 |0 0
|2 NLM Chemicals
|a Aquaporins
650 _ 7 |0 0
|2 NLM Chemicals
|a Capsid Proteins
650 _ 7 |0 0
|2 NLM Chemicals
|a Chaperonin 10
650 _ 7 |0 0
|2 NLM Chemicals
|a Chaperonin 60
650 _ 7 |0 0
|2 NLM Chemicals
|a Eye Proteins
650 _ 7 |0 0
|2 NLM Chemicals
|a Proteins
650 _ 7 |0 0
|2 NLM Chemicals
|a VP6 protein, Rotavirus
650 _ 7 |0 0
|2 NLM Chemicals
|a aquaporin 0
650 _ 7 |a J
|2 WoSType
653 2 0 |2 Author
|a Cryo-EM
653 2 0 |2 Author
|a DireX
653 2 0 |2 Author
|a low resolution
653 2 0 |2 Author
|a flexible fitting
653 2 0 |2 Author
|a real-space refinement
700 1 _ |a Schröder, G.F.
|b 1
|u FZJ
|0 P:(DE-Juel1)132018
773 _ _ |0 PERI:(DE-600)1480801-8
|a 10.1002/bip.22046
|g Vol. 97, p. S687 - S697
|p S687 - S697
|q 97|t Biopolymers
|v 97
|x 0006-3525
|y 2012
|0 PERI:(DE-600)1480801-8
856 7 _ |u http://dx.doi.org/10.1002/bip.22046
909 C O |o oai:juser.fz-juelich.de:111912
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914 1 _ |y 2012
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