VMD-L Mailing List

From: Andrew Dalke (dalke_at_dalkescientific.com)
Date: Wed Jul 16 2008 - 05:45:13 CDT

Giovanni Bellesia:
> I was just wondering (1) what hydropathy scale was considered when the
> macro was built (Kyte and Doolittle one f.e. is quite popular but
> there
> are many others in the literature) and (2) how the scale was
> divided in
>

John Stone replied:
> Offhand I don't know the answer. I think macro was written by
> one of the students in our group eons ago based on older/previous
> hard-coded tables.

I added the original "hydrophobic" definition in the mid-90s. Then
it was the residues FILAPVM, as given in Branden and Tooze (pp6-7 in
the copy I have).

I remember memorizing it as "FILA (the sportsware company) PVM
(the distributed computing library)". I did not include W. I
don't know who added that. B&T calls it "polar".

This page uses the same categories as VMD (including the W):
   http://www.mun.ca/biology/scarr/Amino_acids_nonpolar.html

This adds G:
   http://www.activorcorporation.net/id7.html

This one adds G and Y:
   http://www.geneinfinity.org/sp_aaprops.html

This one adds C but takes away P and A
   http://www.russell.embl-heidelberg.de/aas/hydrophobic.html

                                Andrew
                                dalke_at_dalkescientific.com