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Checkhbond: Hydrogen bond assessment

CheckHBond  evaluates whether a hydrogen bond can be formed between two residues in a PDB structure, allowing you to specify the amino acid present at the second position. The aim of the program is to assess whether a hydrogen bond can be maintained after a mutation has occurred.

Note that because the function of the program is to assess the effects of mutations, it only looks at sidechain/sidechain and sidechain/mainchain hydrogen bonds.

A paper describing the method has been published in Bioinformatics. You can download the paper from Bioinformatics or download the submitted manuscript.

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Upload the PDB file:
Enter the residue identifier for the first residue:	[chain]resnum[insert]
This residue forms its hydrogen bond through:	Sidechain Mainchain donor Nitrogen Mainchain acceptor Oxygen
Enter the residue identifier for the second residue (whose sidechain will be HBonding):	[chain]resnum[insert]
Enter the amino acid type to be checked for the second residue:	(3-letter code)
Cutoff:
Output:	Short   Long

• Residue identifiers should be specified in the form [chain]resnum[insert] where [chain] is an optional chain name and [insert] is an optional insert code. Thus 102, H23, 27A and H52B are all valid residue identifiers.
• The amino acid type should be specified using the three-letter code (upper, lower, or mixed case).
• The cutoff is used to search around overlapping grid points to account for quantization and rounding errors in forming the grids.

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Alison L. Cuff and Andrew C.R. Martin, 2004-6