H Bond Detection Algorithm

Question

[Vijay]

Hello friends, Can you help with telling the algorithm for inferring Hbonds in PDB file. A link of published algo is much appreciated.. Have a nice day!!

[Elmo]

I'm not sure of algorithms, but you can use Pymol to show the Hbonds and its length as well within the structure that you have. Hope that helps.

[Flow]

in the same fashion you could also use MOE (from Chemical Computing Group, $$$) and Discovery Studio (from Accelrys, $$$)

Answer 1

[João Rodrigues]

Hydrogen bonds are usually detected using a combination of distance and angle criteria. Other fancier methods probably exist, but these geometrical solutions are often good enough.

I won't really look for a hydrogen bond paper, Pubmed exists for that, but I will give the link to the GROMACS manual. Look for the Appendix D.35, it has all the ingredients.

Answer 2

[dimkal]

First problem with identifying hydrogen bonbds on a PDB is that, usually, there are no hydrogen atoms included in PDB structures. So your order of operations is:

• Add hydrogen atoms.
  
• Minimize (geometrical optimization) the structure containing the hydrogens. This will optimize hydrogen positions such that there are no spacial overlaps and that they point in the right direction.
• Detect and analyze hydrogen bonds: look at donors/acceptors or total number of hbonds.

You can go about this the open-source route -- using PyMol, VMD, GROMACS (as João had mentioned), Simulaid or MODELLER. Or you can also download Schrodinger's Maestro that I use a lot (usually $$$, but free for academics for MD simulations). There it's really trivial to prepare your protein (add hydrogen atoms/minimization/hbond analysis.)

When you decide on a tool, feel free to post another question to get the recipe.