Sorting the chaff from the wheat at the PDB.
作者信息
Tronrud Dale E, Matthews Brian W
机构信息
Institute of Molecular Biology, Howard Hughes Medical Institute and Department of Physics, University of Oregon, Eugene, OR 97403-1229, USA.
出版信息
Protein Sci. 2009 Jan;18(1):2-5. doi: 10.1002/pro.13.
Abstract
摘要
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本文引用的文献
1
RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation.
Protein Sci. 2009 Jan;18(1):229-39. doi: 10.1002/pro.8.
2
Reexamination of the Three-Dimensional Structure of the Small Subunit of RuBisCo from Higher Plants.
Science. 1989 May 12;244(4905):702-5. doi: 10.1126/science.244.4905.702.
3
Quality of protein crystal structures.
Acta Crystallogr D Biol Crystallogr. 2007 Sep;63(Pt 9):941-50. doi: 10.1107/S0907444907033847. Epub 2007 Aug 17.
4
Crystallography: crystallographic evidence for deviating C3b structure.
Nature. 2007 Aug 9;448(7154):E1-2; discussion E2-3. doi: 10.1038/nature06102.
5
Structure of a bacterial multidrug ABC transporter.
Nature. 2006 Sep 14;443(7108):180-5. doi: 10.1038/nature05155. Epub 2006 Aug 30.
6
X-ray structure of the EmrE multidrug transporter in complex with a substrate.
Science. 2005 Dec 23;310(5756):1950-3. doi: 10.1126/science.1119776.
7
Refined crystal structure of Acinetobacter glutaminasificans glutaminase-asparaginase.
Acta Crystallogr D Biol Crystallogr. 1994 Nov 1;50(Pt 6):826-32. doi: 10.1107/S0907444994003446.
8
Structure of MsbA from E. coli: a homolog of the multidrug resistance ATP binding cassette (ABC) transporters.
Science. 2001 Sep 7;293(5536):1793-800. doi: 10.1126/science.293.5536.1793.
9
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Acta Crystallogr D Biol Crystallogr. 2000 Mar;56(Pt 3):249-65. doi: 10.1107/s0907444999016364.
10
Crystal structure of human serum albumin complexed with fatty acid reveals an asymmetric distribution of binding sites.
Nat Struct Biol. 1998 Sep;5(9):827-35. doi: 10.1038/1869.
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