Question: How to calculate hydrogen bonds of a protein structure from its pdb file?
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gravatar for m.taheri
3.7 years ago by
m.taheri20
Iran, Islamic Republic Of
m.taheri20 wrote:

Hello every body.

My question might seem very basic so excuse me about that. I need to calculate hydrogen bonds of any protein structure from its pdb file. Some pdb files are submitted without hydrogen atoms, like those which are provided with the x-ray crystallography method. I have to write a Java program to calculate hydrogen bonds even from pdb file that miss hydrogen atoms. Does any one know how can I do that specially in Java?

Thanks a lot.

ADD COMMENTlink modified 3.7 years ago by sviatoslav.kendall680 • written 3.7 years ago by m.taheri20
0
gravatar for sviatoslav.kendall
3.7 years ago by
United States
sviatoslav.kendall680 wrote:

This post seems like it might have some useful information: Software For Hydrogen Bond Detection In Pdb Data?

Personally, I would try to do this using PyMol. There is a script in the post I've linked to that seems like it might be pretty adaptable to your goals.

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by sviatoslav.kendall680

Original question sounds like a homework assignment. A program needs to be written in Java.

ADD REPLYlink written 3.7 years ago by genomax75k

Thank you. Of course what I need is the way of calculating hydrogen bonds, namely the algorithm. I know there are so much softwares that can be used for this purpose. But I need to know its algorithm because I should implement it in Java. So any Java program that does it will also be useful.

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by m.taheri20
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