VMD-L Mailing List

From: Ramya Gamini (ramyabhargavi_at_gmail.com)
Date: Thu Mar 05 2009 - 20:20:42 CST

hi!hydropathy index was first proposed by kyte &doolittle (you can google
for some papers, how they arrived at such indexing)

I found some info in the wiki that may be useful for quick reference.
http://en.wikipedia.org/wiki/Hydropathy_index

best
Ramya

On Thu, Mar 5, 2009 at 7:17 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> Yes, they are just a list of residue names.
> You'll see that "hydrophobic" isn't actualy a hard-coded
> atom selection keyword, but rather an atom selection macro:
> vmd > atomselect macro hydrophobic
> resname ALA LEU VAL ILE PRO PHE MET TRP
>
> This one is provided by default in one of the VMD startup
> scripts, it was written by Andrew Dalke, one of the original
> VMD developers, here's his comment on their origination:
>
> # APD's hydrophobic residue list, from Branden and Tooze (pp6-7).
> hydrophobic resname ALA LEU VAL ILE PRO PHE MET TRP
>
> Perhaps someone else can comment on the hydrophobicity in terms
> of a numerical scale as you've asked for.
>
> Cheers,
> John
>
> On Thu, Mar 05, 2009 at 04:58:41PM -0800, Goutham wrote:
> > Hey,
> > I am trying to find the hydrophobicity of the residues in the protein.
> The
> > hydrophobic keyword just acts like a boolean switch. Is there a way to
> find
> > the extent of hydrophobicity?
> >
> > Thanks
> > Goutham
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>