Answers.Body: <p>A quick google search turns up <a href="http://protcalc.sourceforge.net/" rel="nofollow noreferrer">protcalc</a>, which is able to give a nice pH-dependent table of peptide charges (yours ranges from 3.1 at pH 4 to 1.5 at pH 10). It's on sourceforge, so hopefully the source code (and maybe a publication) is somewhere in there. Granted, this isn't R, but it's not clear from your post how necessary that really is.</p>
  
  <p>BTW, in general "best and most accurate" turns out to be highly subjective (at least the "best" part of that).</p>
  
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Answers.Text: Actually somewhere I read that a method to calculate the charge was taking in mind the pkAs of the free amino acids and not the residues on the chain. That's why I wrote "best". I think that the pkA change when the a.a is on the chain. Maybe I should have mentioned it. Also R environment will be preferred.
Answers.UserDisplayName: J. Doe
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Answers.Text: I would be surprised if pH still didn't affect things, though I agree that using a calculation based on free amino acid charges is going to yield wrong values.
Answers.UserDisplayName: Devon Ryan
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Answers.CreationDate: 2017-07-04T13:46:35.560Z
Answers.Text: Taking in mind the pH is standard but pH value is known and can be found. The thing is if there is an algorithm to calculate the pkA of the non free a.a
Answers.UserDisplayName: J. Doe
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Answers.Text: @J.Doe asking for "the best" is not a good question for this site since "the best" is almost always going to be a matter of opinion, and/or depend on the specifics of the sequence you are analyzing. See https://bioinformatics.stackexchange.com/help/dont-ask
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Answers.UserDisplayName: Devon Ryan
Answers.Body: <p>Another quick Google search reveals the <a href="https://cran.r-project.org/web/packages/Peptides/index.html" rel="nofollow noreferrer">Peptides R package</a>.</p>
  
  <pre><code>library(Peptides)
  s &lt;- "RKTTLVPNTQTASPR"
  charge(s)
  
  [1] 2.997683
  </code></pre>
  
  <p>Optional arguments to <code>charge()</code> are <code>pH</code> (default = 7) and <code>pKscale</code> (choice of nine, default = "Lehninger"). See <code>?charge</code> for details.</p>
  
  <p>Another (non-R) option is the <a href="http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/iep.html" rel="nofollow noreferrer">EMBOSS suite program iep</a>. I highly recommend installing EMBOSS, it provides a suite of useful command-line tools with output that can be easily read and processed by other sofware, including R.</p>
  
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Answers.UserDisplayName: neilfws
Answers.Body: <p>I've used PropKa in the past to get isoelectric points. Pretty simple to use:</p>
  
  <p><a href="https://github.com/jensengroup/propka-3.1" rel="nofollow noreferrer">https://github.com/jensengroup/propka-3.1</a></p>
  
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Answers.UserDisplayName: Joe Healey
Body: <p>I was wondering how I can calculate the charge of a protein peptide (e.g. "RKTTLVPNTQTASPR") computationally in R or another tool.</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-04T14:50:33.323Z
Comments.Text: Have you done any search already? What have you found?
Comments.UserDisplayName: jaslibra
Tags: <r><proteins>
Title: Calculating the charge of a peptide computationally
ThreadText: # Calculating the charge of a peptide computationally
  
  (Asked by: username_0 on 2017-07-04)
  
  I was wondering how I can calculate the charge of a protein peptide (e.g. "RKTTLVPNTQTASPR") computationally in R or another tool.
  
  **Tags:** r, proteins
  
  > **Comments:**
  > **username_1**: Have you done any search already? What have you found?  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_2 on 2017-07-04. Score: 3
  
  A quick google search turns up [protcalc](http://protcalc.sourceforge.net/), which is able to give a nice pH-dependent table of peptide charges (yours ranges from 3.1 at pH 4 to 1.5 at pH 10). It's on sourceforge, so hopefully the source code (and maybe a publication) is somewhere in there. Granted, this isn't R, but it's not clear from your post how necessary that really is.
  
  BTW, in general "best and most accurate" turns out to be highly subjective (at least the "best" part of that).
  
  > **Comments:**
  > **username_0**: Actually somewhere I read that a method to calculate the charge was taking in mind the pkAs of the free amino acids and not the residues on the chain. That's why I wrote "best". I think that the pkA change when the a.a is on the chain. Maybe I should have mentioned it. Also R environment will be preferred.  
  > **username_2**: I would be surprised if pH still didn't affect things, though I agree that using a calculation based on free amino acid charges is going to yield wrong values.  
  > **username_0**: Taking in mind the pH is standard but pH value is known and can be found. The thing is if there is an algorithm to calculate the pkA of the non free a.a  
  > **username_3**: @username_0 asking for "the best" is not a good question for this site since "the best" is almost always going to be a matter of opinion, and/or depend on the specifics of the sequence you are analyzing. See https://bioinformatics.stackexchange.com/help/dont-ask  
  
  ---
  
  ### Answer by username_4 on 2017-07-18. Score: 3
  
  Another quick Google search reveals the [Peptides R package](https://cran.r-project.org/web/packages/Peptides/index.html).
  
  ```
  library(Peptides)
  s <- "RKTTLVPNTQTASPR"
  charge(s)
  
  [1] 2.997683
  
  ```
  
  Optional arguments to `charge()` are `pH` (default = 7) and `pKscale` (choice of nine, default = "Lehninger"). See `?charge` for details.
  
  Another (non-R) option is the [EMBOSS suite program iep](http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/iep.html). I highly recommend installing EMBOSS, it provides a suite of useful command-line tools with output that can be easily read and processed by other sofware, including R.
  
  
  ---
  
  ### Answer by username_5 on 2017-07-05. Score: 1
  
  I've used PropKa in the past to get isoelectric points. Pretty simple to use:
  
  <https://github.com/jensengroup/propka-3.1>
  
  
  ---
  
  