Question: H Bond Detection Algorithm
gravatar for Vijay
5.6 years ago by
Vijay20 wrote:

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!!

pdb algorithm • 1.6k views
ADD COMMENTlink written 5.6 years ago by Vijay20

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.

ADD REPLYlink written 5.6 years ago by Elmo110

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

ADD REPLYlink written 5.6 years ago by Flow1.5k
gravatar for João Rodrigues
5.6 years ago by
João Rodrigues2.4k
Stanford University, U
João Rodrigues2.4k wrote:

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.

ADD COMMENTlink written 5.6 years ago by João Rodrigues2.4k
gravatar for dimkal
5.6 years ago by
United States
dimkal730 wrote:

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.

ADD COMMENTlink written 5.6 years ago by dimkal730
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