Checkhbond: Hydrogen bond assessment

Availability

03.01.14 APOLOGIES! Our web server went down at the start of the Christmas break when there was a power outage. This killed the power supply and one of the disks so it has only come up again today when the IT staff have come back from the Christmas closure.

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)
Cutoff:
Output: Short   Long


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