How can I calculate hydrogen bonds in a specific direction w.r.t. a C-alpha atom in a protein?
1
0
Entering edit mode
6 weeks ago
user366312 ▴ 10

I need to calculate H-bonds in a specific direction of a C-alpha atom of a protein. And, I need to calculate that from a PDB file.

Can anyone give me an idea regarding how to do that?

N.B. I need to write a python program.

python hydrogen-bonds pdb-file proteins • 498 views
ADD COMMENT
0
Entering edit mode
6 weeks ago
Mensur Dlakic ★ 15k

If I understand correctly what you need - and it wouldn't hurt if you elaborated a bit - this is somewhat similar to half-sphere exposure (HSE), which calculates protein residue's solvent accessibility on the opposite sides of a C-alpha atom. There is a paper about it:

https://pubmed.ncbi.nlm.nih.gov/15688434/

And there is a BioPython code to calculate it:

https://biopython.org/docs/dev/api/Bio.PDB.HSExposure.html

This may give you some idea how to approach the problem, but it requires a thorough understanding of protein structure

ADD COMMENT
0
Entering edit mode

the keyword in my question was "hydrogen bond". your supplied links do not say anything about hydrogen bonds.

ADD REPLY
0
Entering edit mode

I can read you keywords. I can also read this part:

Can anyone give me a general direction/idea regarding how to do that?

I said clearly that the links are about solvent accessibility, which is to say that I tried to give you a general idea. You can try that, or stock up with popcorn and soda and wait for someone to give you a complete solution.

ADD REPLY
0
Entering edit mode

I am sorry but your answer is not helpful. You are trying to explain a cat using a dog.

ADD REPLY

Login before adding your answer.

Traffic: 1789 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