What are the properties that can be derived from an amino acid sequence apart from those mentioned in the website? In the mentioned website, the properties that can be calculated from amino acid sequence are:

1. Molecular weight of protein
2. Number of amino acids in the protein sequnece
3. Composition of charged residues (DEKHR)
4. Composition of aliphatic residues (ILV)
5. Composition of Aromatic residues (FHWY)
6. Composition of Polar residues (DERKQN)
7. Composition of Neutral residues (AGHPSTY)
8. Composition of Hydrophobic residues (CVLIMFW)
9. Composition of Positive charged residues (HKR)
10. Composition of Negative charged residues (DE)
11. Composition of tiny residues (ACDGST)
12. Composition of Small residues (EHILKMNPQV)
13. Composition of Large residues (FRWY)

  • $\begingroup$ Other than the first two, the rest of the groups seems like a list of binary sets based on specific chemical properties of the amino acids. Without any additional information, this question is too broad. $\endgroup$ – March Ho Sep 4 '15 at 9:01
  • $\begingroup$ what additional information do you want. please tell me. Dont just close it. I need this question open. $\endgroup$ – girl101 Sep 4 '15 at 9:42
  • $\begingroup$ What exactly do you define as a "property"? The current list is not well defined, and arguably silly examples like "Composition of residues with "E" in their name" are also "properties". $\endgroup$ – March Ho Sep 4 '15 at 10:02
  • $\begingroup$ This approach (that you linked to), wherein one takes a purified protein and subjects it to amino acid analysis (or amino acid composition), dates back to a period in time from ~ 1960-1980. Once molecular cloning was developed it became much faster to clone the gene for a protein to determine its identify rather than sequence the polypeptide itself. Around the same time a gas-phase chromatography device was coupled to a mass spectrometer and marketed commercially by Applied Biosystems, permitting so-called microsequencing of peptide fragments. BLAST is going to be way more sensitive. $\endgroup$ – mdperry Sep 5 '15 at 20:52
  • $\begingroup$ Sensitive as in? $\endgroup$ – girl101 Sep 6 '15 at 4:13

Just look at NCBI , EMBL and DDJB tools. These three are premier and global database centres. Their tools are self explanatory. You can calculate lot of things from these sequences. Besides these there are many in house tools for calculating specific information from sequences from many bioinformatics research labs across the world.

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Using a helical wheel projection you can make predictions of regions that are likely to form, or adopt, amphipathic helices. These are alpha-helices where one face, or side, of the helix is largely polar while the opposite, side, or face, of the helix is largely non-polar.

Also, based on known X-Ray crystal structures, there are some residues that are known as helix breakers, like Pro and Gly, and there are other residues that are often found in beta sheets, so you can make secondary structure predictions, based on the primary amino acid sequence.

However, in the absence of extended regions of amino acid sequence identity, these predictions are just hypotheses.

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  • $\begingroup$ No, i don't want to predict anything, i want confirmed properties, not predictions $\endgroup$ – girl101 Sep 4 '15 at 5:44
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    $\begingroup$ Good luck with that. $\endgroup$ – mdperry Sep 4 '15 at 12:23

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