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abYsis which allows most of our antibody analysis to be performed is still available at www.abysis.org

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.

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)
Output: Short   Long

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