How to calculate hydrogen bonds of a protein structure from its pdb file?
1
0
Entering edit mode
5.1 years ago
m.taheri ▴ 40

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.

pdb file protein hydrogen bonds • 3.2k views
ADD COMMENT
0
Entering edit mode
5.1 years ago

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 COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 2481 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6