Hi Shane,
I think I meant weblogo which shows frequency of amino acids....
e.g. http://weblogo.berkeley.edu/
Sorry for the confusion
J
_________________________________
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa
Ph / Waea +64 3 4797293
Fax / Waeawhakaahua +64 3 4797034
From: Shane Neeley [mailto:shane.nee...@gmail.com]
Sent: Wednesday, 4 April 2012 10:18 a.m.
To: Joel Tyndall
Subject: Re: [PyMOL] Protein Parameters?
Hi Thanks for the tip Joel.
I checked a few of the sequences for protein motifs but because they are so
sort and because there really is no known function, i think it is unlikely to
have any hits.
On Tue, Apr 3, 2012 at 2:58 PM, Joel Tyndall
<joel.tynd...@otago.ac.nz<mailto:joel.tynd...@otago.ac.nz>> wrote:
Hi Shane,
Whilst I am no expert, I would think possible a sequence motif (based on amino
acid composition) may help. It may show up certain amino acids at specific
points. Given the short length of the peptides, the question is what are they
used for?
Hope this helps
_________________________________
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa
Ph / Waea +64 3 4797293<tel:%2B64%203%204797293>
Fax / Waeawhakaahua +64 3 4797034<tel:%2B64%203%204797034>
From: Shane Neeley
[mailto:shane.nee...@gmail.com<mailto:shane.nee...@gmail.com>]
Sent: Wednesday, 4 April 2012 3:58 a.m.
To: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: [PyMOL] Protein Parameters?
Hi,
This is unrelated to PyMol, but I just wanted to spam the community to see what
they think about different protein parameters. Let me know if this sort of
question is inappropriate for the forum.
I have thousands of randomly generated 7 amino acid peptide sequences that are
within a virus. As we subject this virus to reproduction selective pressure in
cell lines, we get back functional viruses with certain 7 amino acid sequences,
while most random sequences are null mutations. So I am now testing the the
positive sequences to see what they have in common, or what is most important.
I am doing this with a likely structural sequence and a likely surface sequence.
So far I have these params from http://web.expasy.org/protparam/ and ConSurf
1) Isoelectric Point
2) Molecular Weight (may mean bulkiness)
3) GRAVY: grand average of hydropathicity
4) Conservation of AAs at given locations
Do any of you protein experts know of other parameters that I could be testing?
Maybe something like Phi-value analysis?
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