How To Calculate The Net Charge Of Amino Acids *Sequences/Peptides* At Ph 7 Using R?

Question

[bioinfo12]

Hi,

I would like to calculate the net charge of amino acids at pH 7. Is there any R package available for this calculation? Edit: op wants the charge of a sequence, not single AA

Answer 1

[Michael]

There is nothing to calculate, this is textbook knowledge about amino acids, there are amino acids with charged and uncharged side chains. Just look up the charges in Wikipedia http://en.wikipedia.org/wiki/Amino_acid

Edit: you can simply count the positively and negatively charged AAs in the sequence, the difference is the charge of the sequence.

[bioinfo12]

@Michael I am really sorry for my incorrect question.

Answer 2

[seidel]

I think you're looking for either of two things. I disagree with Michael that there is nothing to calculate. On one hand, you could make a sort of lookup table using a named array of the amino acids and their pK values, then at any given pH you could access the value and assess the direction of charge. However you might actually be asking something else. At any given pH, only a fraction of any amino acids exist in a given charged state, so perhaps by "net charge" you're looking for the relatives proportion of charge at that pH? In that case I'm not aware of a package (I haven't looked), but it wouldn't be that hard to write a function for the Henderson-Hasselbalch equation (complete with amino acid pK lookup table), that returns this value for any pH. It would only be a few lines of simple code.

[bioinfo12]

Thank you for your answer. I would like to calculate the net charge of amino acid sequence. I am not a programmer. Is there any software available to calculate the net charge from the amino acid sequences?

[Michael]

You should have written that immediately in your question. That is ofc something very different.

[abi]

I thought as well too that bionfo12 meant net charge of an peptide. Pathetic with poorly framed questions!! What is really sad is that there are people out here trying to help others out and in the end it turns out that it has been a waste of time for them just because of a poorly framed question!!

[Michael]

I don't bother too much, people are themselves responsible to pose their question correctly. If they don't the answers are not going to help them, if they really need a good answer, they will come back, if not, no damage done except for the poster.

I only answer if I have time to spare and I know misunderstanding can happen, so for me it's not a waste of time.

[Michael]

You could speculate a lot about what a question really means. I prefer to not do that and answer the literal question if possible. In this case the original question was quite clearly phrased, but unfortunately, the terms were used incorrectly. So, bad question lead to incorrect answer, that's what happened.

Answer 3

[Neilfws]

You can calculate net charge of a protein sequence using the seqinr package. See the example function computeCharge() on page 133 of the manual (PDF).

[Michael]

Good, that's more reliable than trying to code this yourself! There should be functions in bioperl and bio python too.

[Neilfws]

I expect so, but OP asked for an R package.