[Jalview-discuss] Hydrophobicity and similar values

Geoff Barton gjbarton at dundee.ac.uk
Wed Jan 6 12:12:51 GMT 2016

As Mungo says, Jalview provides a variety of ways to calculate 
properties from **sequences** (that could be read in from a PDB file) 
but does not provide an overall average.   There are some overall 
properties calculated from sequences available from the expasy.ch 
website that might do what you want.  In addition, our TarO server (See 
www.compbio.dundee.ac.uk for links)  will also calculate properties 
given a single sequence (e.g. GRAVY and predicted pI).  Again, these are 
just from the sequence and take no account of the structural environment 
of the amino acids.

I hope this helps.


On 06/01/2016 12:04, Mungo Carstairs (Staff) wrote:
> Hello Celia,
> The short answer is no -  Jalview does not compute values for these 
> properties, so has no data that could be averaged over the structure 
> for them.
> Jalview /does/ have built-in sequence colour schemes for 
> hydrophobicity, helix propensity, and buried index (see 
> http://www.jalview.org/help/html/colourSchemes/index.html), but these 
> are based only on the amino acid residues (a global average), not on 
> their context in the specific structure.
> Dedicated structure viewers (Jalview supports integration with Chimera 
> and Jmol) may have some capability to provide what you are after, but 
> I will have to leave that to others more expert in those tools to 
> comment on &#X1f609.
> Best regards,
> Mungo
> Mungo Carstairs
> Jalview Computational Scientist
> The Barton Group
> Division of Computational Biology
> School of Life Sciences
> University of Dundee, Dundee, Scotland, UK.
> www.jalview.org <http://www.jalview.org/>
> www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk/>
> ------------------------------------------------------------------------
> *From:* jalview-discuss-bounces at jalview.org 
> <jalview-discuss-bounces at jalview.org> on behalf of Kun Rodrigues, 
> Celia <celia.rodrigues at ucl.ac.uk>
> *Sent:* 05 January 2016 16:36
> *To:* jalview-discuss at jalview.org
> *Subject:* [Jalview-discuss] Hydrophobicity and similar values
> Dear Jalview Administrator,
> If, given a pdb file, could Jalview give me average values of 
> hydrophobicity, polarity, maybe propensity to be buried or to form 
> helix, or maybe even surface or active centre accessibility for the 
> whole protein structure? I just want one value for the whole structure.
> Thank you,
> Celia
> The University of Dundee is a registered Scottish Charity, No: SC015096
> _______________________________________________
> Jalview-discuss mailing list
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Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology
School of Life Sciences | University of Dundee, Scotland, UK | g.j.barton at dundee.ac.uk
Tel: +44 1382 385860 | www.compbio.dundee.ac.uk | twitter: @gjbarton

The University of Dundee is registered Scottish charity: No.SC015096

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