I am using a model designed with modeller to do docking. Howevere there is problem with ligand design. The ligand is gogin to be 4 peptides long and start with Ser,Ala, Gly , Val or CYS. The amino acids in the other postion should be any amino acid. How can I design a peptide with 20**3 different amino acids. Or can you point me to a software that do ligand desing or a good database.
Knut J _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969
On 3/2/10 6:50 AM, Knut J Bjuland wrote: > I am using a model designed with modeller to do docking. Howevere there > is problem with ligand design. The ligand is gogin to be 4 peptides long > and start with Ser,Ala, Gly , Val or CYS. The amino acids in the other > postion should be any amino acid. How can I design a peptide with 20**3 > different amino acids. Or can you point me to a software that do ligand > desing or a good database.
The last time you asked this question I told you that Modeller didn't do protein design, and pointed you to Rosetta's design module:
http://salilab.org/archives/modeller_usage/2010/msg00051.html
Was that not suitable?
Ben Webb, Modeller Caretaker
Ditto for Pymol, etc
_________________________________ 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
-----Original Message----- From: modeller_usage-bounces@salilab.org [mailto:modeller_usage-bounces@salilab.org] On Behalf Of Modeller Caretaker Sent: Wednesday, 3 March 2010 5:26 a.m. To: Knut J Bjuland Cc: modeller_usage@salilab.org Subject: Re: [modeller_usage] ligand desgin
On 3/2/10 6:50 AM, Knut J Bjuland wrote: > I am using a model designed with modeller to do docking. Howevere there > is problem with ligand design. The ligand is gogin to be 4 peptides long > and start with Ser,Ala, Gly , Val or CYS. The amino acids in the other > postion should be any amino acid. How can I design a peptide with 20**3 > different amino acids. Or can you point me to a software that do ligand > desing or a good database.
The last time you asked this question I told you that Modeller didn't do protein design, and pointed you to Rosetta's design module:
http://salilab.org/archives/modeller_usage/2010/msg00051.html
Was that not suitable?
Ben Webb, Modeller Caretaker
I had difficulties running RosettaDesign plugin in Pymol, due to insufficient documentation (not sure about what executable it needs, neither which version - the plugin is not included in v3.0++, etc).
Found the server much easier provided you're patient enough...
http://rosettadesign.med.unc.edu/index.html
2010/3/2 Joel Tyndall joel.tyndall@otago.ac.nz
> Ditto for Pymol, etc > > _________________________________ > 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 > > > -----Original Message----- > From: modeller_usage-bounces@salilab.org [mailto: > modeller_usage-bounces@salilab.org] On Behalf Of Modeller Caretaker > Sent: Wednesday, 3 March 2010 5:26 a.m. > To: Knut J Bjuland > Cc: modeller_usage@salilab.org > Subject: Re: [modeller_usage] ligand desgin > > On 3/2/10 6:50 AM, Knut J Bjuland wrote: > > I am using a model designed with modeller to do docking. Howevere there > > is problem with ligand design. The ligand is gogin to be 4 peptides long > > and start with Ser,Ala, Gly , Val or CYS. The amino acids in the other > > postion should be any amino acid. How can I design a peptide with 20**3 > > different amino acids. Or can you point me to a software that do ligand > > desing or a good database. > > The last time you asked this question I told you that Modeller didn't do > protein design, and pointed you to Rosetta's design module: > > http://salilab.org/archives/modeller_usage/2010/msg00051.html > > Was that not suitable? > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >
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Joel Tyndall -
Knut J Bjuland -
Modeller Caretaker -
Thomas Evangelidis