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. 2004 Jun 4:5:69.
doi: 10.1186/1471-2105-5-69.

pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files

Thomas Lütteke  1 , Claus-W von der Lieth
Affiliations

pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files

Thomas Lütteke et al. BMC Bioinformatics. .

Abstract

Background: Carbohydrates are involved in a variety of fundamental biological processes and pathological situations. They therefore have a large pharmaceutical and diagnostic potential. Knowledge of the 3D structure of glycans is a prerequisite for a complete understanding of their biological functions. The largest source of biomolecular 3D structures is the Protein Data Bank. However, about 30% of all 1663 PDB entries (version September 2003) containing carbohydrates comprise errors in glycan description. Unfortunately, no software is currently available which aligns the 3D information with the reported assignments. It is the aim of this work to fill this gap.

Results: The pdb-care program http://www.glycosciences.de/tools/pdb-care/ is able to identify and assign carbohydrate structures using only atom types and their 3D atom coordinates given in PDB-files. Looking up a translation table where systematic names and the respective PDB residue codes are listed, both assignments are compared and inconsistencies are reported. Additionally, the reliability of reported and calculated connectivities for molecules listed within the HETATOM records is checked and unusual values are reported.

Conclusion: Frequent use of pdb-care will help to improve the quality of carbohydrate data contained in the PDB. Automatic assignment of carbohydrate structures contained in PDB entries will enable the cross-linking of glycobiology resources with genomic and proteomic data collections.

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Figures

Figure 1
Figure 1
Description of carbohydrate structures (a) Typical PDB-entry (PDB-code: 1axy) with an attached N-Glycan given in spacefilling representation. (b) Ball-and-Stick 3D-representation of the same N-Glycan. For a simple comparison of the different representations, the same colour code for each residue is used for Figure 1b-d. (c) LINUCS representation of the same N-Glycan structure. (d) IUPAC-like description of the same N-Glycan.
Figure 2
Figure 2
Erroneous connections in PDB entries. Besides missing connection information, some entries contain surplus connections. (a) In case the wrongly connected atoms are far distant from each other, these errors can be observed on the first view (PDB entry 1qoo, residue NAG401A). In this example, the spuriously assigned connections result in a hexavalent carbon atom. (b) Surplus connections ranging on short distances are much more difficult to discover by visual inspection (PDB entry 1bcs, residues NAG1051, NAG1052).
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References

    1. Rademacher TW, Parekh RB, Dwek RA. Glycobiology. Annu Rev Biochem. 1998;57:785–838. doi: 10.1146/annurev.bi.57.070188.004033. - DOI - PubMed
    1. Taylor ME, Drickamer K. Introduction to Glycobiology. Oxford University Press; 2002. p. 224.
    1. Varki A, Esko J, Freeze H, G. Hart, J. Marth. Essential of Glycobiology. New York, Cold Spring Habor Laboratory Press; 1999. - PubMed
    1. Apweiler R, Hermjakob H, Sharon N. On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. Biochim Biophys Acta. 1999;1473:4–8. doi: 10.1016/S0304-4165(99)00165-8. - DOI - PubMed
    1. Ben-Dor S, Esterman N, Rubin E, Sharon N. Biases and complex patterns in the residues flanking protein N-glycosylation sites. Glycobiology. 2004;14:95–101. doi: 10.1093/glycob/cwh004. - DOI - PubMed

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