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

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From: Shane Neeley [mailto:shane.neeley@gmail.com]
Sent: Wednesday, 4 April 2012 3:58 a.m.
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Protein Parameters?




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?