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pdb-care: PDB CArbohydrate REsidue check

Introduction
A recent study revealed that about 30% of the carbohydrate-containing PDB entries comprise at least one error within the carbohydrate moieties [1].
To reduce this high rate of errors in further entries, pdb-care aids experimentalists in detecting discrepancies in connectivities and nomenclature.

A beta-version of a new, improved version of pdb-care is available now. Please consider that this is a beta-version and thus still contains some errors.

Contact: Thomas Lütteke

References

Enter PDB ID: (⇒Examples)

or select file to upload:

or insert pdb-file below:

Select Options:

Find carbohydrates in
Assign connections by atom distances

Choose checks to perform:

Connections
	Bond length / valence check
	Tolerance:
	Ignore connections to ions
	Connections between ions and other residues are mostly no covalent bonds but complex bond. Therefore, they should be ignored when checking bond lengths and atom valences.
Nomenclature
	Check carbohydrate residue nomenclature
	Since erroneous residue naming is by far the most common type of error detected in carbohydrate structures within the PDB, it is strongly recommended to perform this check on carbohydrate-containing structures. Additional nomenclature options: Find correct nomenclature for mismatched residues or residues unknown to pdb-care.

Description of output and examples

References

[1]	Lütteke T , Frank M , von der Lieth CW: Data mining the Protein Data Bank: Automatic detection and assignment of carbohydrate structures. Carbohydrate Research 2004, 339(5): 1015-1020.

When citing pdbcare, please refer to:

Lütteke T, von der Lieth CW:
pdb-care (PDB CArbohydrate REsidue check): a program to support annotation of complex carbohydrate structures in PDB files
BMC Bioinformatics 2004, 5: 69.