Checkhbond: Hydrogen bond assessment

Availability - IMPORTANT

Our servers will be shut down 15.08.08 from 2pm and will be unavailable until the morning of 18th August.
This is because of a scheduled electrical shutdown.

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.

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.

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

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