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Calculate molecular weight in Kda from protein sequence

Calculate molecular weight in Kda from protein sequence - Bioinformatics

Calculate molecular weight in Kda from protein sequence - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


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Old 06-13-2012, 10:29 AM
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Default Calculate molecular weight in Kda from protein sequence



thank you for taking the time to look at my post. I was wondering if there is anyone who could help me to calculate the molecular weight of a protein from the protein sequence, ideally manually. I heard that for a rough estimate the following can be used:

No. of amino acids * 110 (i.e. the average mol wt of an amino acid) - No of amino acids * 18 (i.e mol wt of water)

I am also aware that there are numerous web servers available to do this, however, I have many hundreds of thousands of sequences and I want to incorporate this into my programs which performs other calculations.

If you cannot help with this, could you suggest an accurate stand alone program that I can use via a commandline call to do this?

Many thanks for your time.
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Old 08-16-2012, 04:36 AM
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Default Re: Calculate molecular weight in Kda from protein sequence

I guess the formula you quoted is the one which would give you the right answer.
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Old 08-16-2012, 04:25 PM
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Default Re: Calculate molecular weight in Kda from protein sequence

Quote:
Originally Posted by kajendiran View Post
thank you for taking the time to look at my post. I was wondering if there is anyone who could help me to calculate the molecular weight of a protein from the protein sequence, ideally manually. I heard that for a rough estimate the following can be used:

No. of amino acids * 110 (i.e. the average mol wt of an amino acid) - No of amino acids * 18 (i.e mol wt of water)

I am also aware that there are numerous web servers available to do this, however, I have many hundreds of thousands of sequences and I want to incorporate this into my programs which performs other calculations.

If you cannot help with this, could you suggest an accurate stand alone program that I can use via a commandline call to do this?

Many thanks for your time.
There are pre-existing databases of protein names and molecular weights (UniProt for instance). You could take the names and masses and put them into your software. Alternatively you could write a script to accurately calculate the mass (given an input sequence). You just need to look up the mass of the different amino acids. The formula you show will not be very accurate in some cases because not all proteins have an evenly distributed amino acid content.
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Old 08-17-2012, 03:39 AM
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Arrow Re: Calculate molecular weight in Kda from protein sequence

Hi


Solution from Mmorgan is quite useful and refine .

Go through below link It May helps you.

[Only registered users see links. ]

Regards
Kunal Pandya
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