Sequence‐structure mapping errors in the PDB: OB‐fold domains
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[1] A. Goldman,et al. Toward a quantum-mechanical description of metal-assisted phosphoryl transfer in pyrophosphatase , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[2] J. Thornton,et al. PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .
[3] C. W. Hilbers,et al. Sequence-specific 1H-NMR assignment and secondary structure of the Tyr41----His mutant of the single-stranded DNA binding protein, gene V protein, encoded by the filamentous bacteriophage M13. , 1991, European journal of biochemistry.
[4] A. Murzin. OB(oligonucleotide/oligosaccharide binding)‐fold: common structural and functional solution for non‐homologous sequences. , 1993, The EMBO journal.
[5] B. Luisi,et al. A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation. , 2000, Structure.
[6] A. McPherson,et al. Refined structure of the gene 5 DNA binding protein from bacteriophage fd. , 1983, Journal of molecular biology.
[7] C Sander,et al. Mapping the Protein Universe , 1996, Science.
[8] D. Eisenberg,et al. Assessment of protein models with three-dimensional profiles , 1992, Nature.
[9] J. Rullmann,et al. Quality assessment of NMR structures: a statistical survey. , 1998, Journal of molecular biology.
[10] E. G Arutiunian,et al. X-Ray Diffraction Study of Inorganic Pyrophosphatase from Baker,S Yeast at the 3 Angstroms Resolution (Russian) , 1983 .
[11] Ceslovas Venclovas,et al. Comparative modeling in CASP5: Progress is evident, but alignment errors remain a significant hindrance , 2003, Proteins.
[12] Cheng Yang,et al. Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 Å resolution , 1997, Nature Structural Biology.
[13] T. Tsukihara,et al. Roles of functional loops and the C-terminal segment of a single-stranded DNA binding protein elucidated by X-Ray structure analysis. , 2000, Journal of biochemistry.
[14] C. Sander,et al. Errors in protein structures , 1996, Nature.
[15] T C Terwilliger,et al. Structure of the gene V protein of bacteriophage f1 determined by multiwavelength x-ray diffraction on the selenomethionyl protein. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[16] Adam Zemla,et al. Critical assessment of methods of protein structure prediction (CASP)‐round V , 2005, Proteins.
[17] T. Blundell,et al. Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.
[18] G. Waksman,et al. Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[19] C Venclovas,et al. Comparative modeling of CASP4 target proteins: Combining results of sequence search with three‐dimensional structure assessment , 2001, Proteins.
[20] M. Vijayan,et al. Structure of Mycobacterium tuberculosis single-stranded DNA-binding protein. Variability in quaternary structure and its implications. , 2003, Journal of molecular biology.
[21] M. Sippl. Recognition of errors in three‐dimensional structures of proteins , 1993, Proteins.
[22] Patrice Koehl,et al. The ASTRAL compendium for protein structure and sequence analysis , 2000, Nucleic Acids Res..
[23] C. Sander,et al. Protein structure comparison by alignment of distance matrices. , 1993, Journal of molecular biology.
[24] R. Varadarajan,et al. Discrepancies between the NMR and X-ray structures of uncomplexed barstar: analysis suggests that packing densities of protein structures determined by NMR are unreliable. , 1998, Biochemistry.
[25] Eugene V. Koonin,et al. SEALS: A System for Easy Analysis of Lots of Sequences , 1997, ISMB.
[26] A G Murzin,et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.
[27] Axel T. Brunger,et al. X-PLOR Version 3.1: A System for X-ray Crystallography and NMR , 1992 .
[28] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[29] D. Higgins,et al. T-Coffee: A novel method for fast and accurate multiple sequence alignment. , 2000, Journal of molecular biology.
[30] Leszek Rychlewski,et al. Fold-recognition detects an error in the Protein Data Bank , 2002, Bioinform..
[31] M. Totrov,et al. Contact area difference (CAD): a robust measure to evaluate accuracy of protein models. , 1997, Journal of molecular biology.
[32] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[33] G. Waksman,et al. Structure of the DNA binding domain of E. coli SSB bound to ssDNA , 2000, Nature Structural Biology.
[34] J. Thornton,et al. Stereochemical quality of protein structure coordinates , 1992, Proteins.
[35] D. Moras,et al. Crystal structure of aspartyl‐tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation , 1998, The EMBO journal.