[Bioperl-l] amino acid index

[Navdeep Jaitly]

Hi Ewan!
The AAIndex basically a database of different physiochemical/biological 
properties of individual Amino Acids ( such as hydrophobicity, flexibility, 
surface probability, etc) as calculated by different people from different 
experiments. Each Amino acid is given a relative value for a certain 
property. For example Alanine is given 0.61 and lysine is assigned a value 
of 1.15 for their respective hydrophobicities. These  values can be 
calculated for a peptide by summing up the contributions  of the individual 
amino acids in the peptide.
The Kawashima lab at the Institute for Chemical Research at Japan basically 
compiled the AAIndex database from literature and have put them together at 
http://www.genome.ad.jp/dbget/aaindex.html
These properties can be very useful if you are trying to correlate 
properties of peptides with something you have observed experimentally. A 
simplistic example would be to try and correlate hydrophobicity for a 
peptide and its elution time in reverse phase HPLC.
People often use the properties extensively in different areas, say protein 
secondary prediction (where there is a high correlation between charge, 
hydrophobicity, flexbility and secondary structures like coils) , epitope 
prediction (correlations with secondary structure, hydrophobicity, surface 
probability, etc), etc. However, it can be limiting to use just one property 
of the amino acids when you are exploring new relationships. Switching the 
property to test a different one can be time consuming, and I figured it 
would be useful to have this possibility in bioperl.
Cheers!



>From: Ewan Birney <birney@ebi.ac.uk>
>Reply-To: birney@ebi.ac.uk
>To: Navdeep Jaitly <ndjaitly@hotmail.com>
>CC: bioperl-l@bioperl.org
>Subject: Re: [Bioperl-l] amino acid index
>Date: Thu, 4 Jul 2002 13:26:20 -0400 (EDT)
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>On Wed, 3 Jul 2002, Navdeep Jaitly wrote:
>
> > Hi!
> > Is there any on-going work that would allow users to calculate AAIndex
> > values for a peptide by specifying an accession number for an AAIndex ?
> > Cheers!
>
>Deep - what is an AAIndex value - I'm just ignorant of what it is and what
>people use it for?
>
>
> > Deep
> >
> >
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