[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? -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Protein Parameters?
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 Fax / Waeawhakaahua +64 3 4797034 From: Shane Neeley [mailto:shane.nee...@gmail.com] Sent: Wednesday, 4 April 2012 3:58 a.m. To: 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? -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Protein Parameters?
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.nzmailto: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 4797293tel:%2B64%203%204797293 Fax / Waeawhakaahua +64 3 4797034tel:%2B64%203%204797034 From: Shane Neeley [mailto:shane.nee...@gmail.commailto:shane.nee...@gmail.com] Sent: Wednesday, 4 April 2012 3:58 a.m. To: pymol-users@lists.sourceforge.netmailto: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? -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
