Hi-
Although I'm not a very regular user of modeller, I believe it is well known that long gaps, especially terminal gaps, look strange when modeled using default options. I was wondering, would be possible to add an Rg restraint so that such regions at least stay nearby the rest of the (well-modeled) protein? This is not just a problem of aesthetics. When I try to superimpose such structures using structural alignment, sometimes the long gappy regions throw the superpositioning calculation off. I could just write a script to try to cut them out, but it would be nice if I could fix the problem at the source. My suggestion of using an Rg restrain would be basically
"if distance of residue x from center is greater than some huge value (2-3x the predicted Rg, based on sequence length), add a bias to the potential for x toward the center of the protein"
This kind of restraint should leave the "good" parts of the alone and just pull the "bad" parts closer to the rest of the protein.
Any thoughts on whether this can be done?
Thanks for your advice and apologies if I have raised a already well-discussed topic.
Regards,
Daron
On 05/30/2013 02:31 AM, Daron Standley wrote: > Although I'm not a very regular user of modeller, I believe it is well > known that long gaps, especially terminal gaps, look strange when > modeled using default options.
Sure. Typically, we just remove those regions and don't model them. Any modeling of these regions is just going to be fantasy anyway.
> "if distance of residue x from center is greater than some huge value > (2-3x the predicted Rg, based on sequence length), add a bias to the > potential for x toward the center of the protein"
The easiest way to do that would be to add an upper bound distance restraint between each C alpha and the center of gravity of the protein. An example is at http://salilab.org/modeller/9.11/manual/node105.html
Ben Webb, Modeller Caretaker
Hi,
Allow me add one more option in this case. You can use a web server that make secondary structure predictions from sequence, e.g. PsiPred (http://bioinf.cs.ucl.ac.uk/psipred/) and use the result to impose any restrictions in the protein modelling, such as alpha helices or beta-sheet.
Regards,
------------------------------------- Flavio Augusto Vicente Seixas Laboratory of Structural Biochemistry Department of Biochemistry Universidade Estadual de Maringá, PR, Brazil http://www.uem.br
--- On Thu, 5/30/13, Modeller Caretaker modeller-care@salilab.org wrote:
> From: Modeller Caretaker modeller-care@salilab.org > Subject: Re: [modeller_usage] Question about huge gaps > To: "Daron Standley" standley@ifrec.osaka-u.ac.jp > Cc: modeller_usage@salilab.org > Date: Thursday, May 30, 2013, 7:35 PM > On 05/30/2013 02:31 AM, Daron > Standley wrote: > > Although I'm not a very regular user of modeller, I > believe it is well > > known that long gaps, especially terminal gaps, look > strange when > > modeled using default options. > > Sure. Typically, we just remove those regions and don't > model them. Any modeling of these regions is just going to > be fantasy anyway. > > > "if distance of residue x from center is greater than > some huge value > > (2-3x the predicted Rg, based on sequence length), add > a bias to the > > potential for x toward the center of the protein" > > The easiest way to do that would be to add an upper bound > distance restraint between each C alpha and the center of > gravity of the protein. An example is at > http://salilab.org/modeller/9.11/manual/node105.html > > Ben Webb, Modeller Caretaker > -- modeller-care@salilab.org > http://www.salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >
Dear Ben,
Thanks Ben,
That's exactly what I needed to know!
Daron
On May 31, 2013, at 3:35 AM, Modeller Caretaker modeller-care@salilab.org wrote:
> On 05/30/2013 02:31 AM, Daron Standley wrote: >> Although I'm not a very regular user of modeller, I believe it is well >> known that long gaps, especially terminal gaps, look strange when >> modeled using default options. > > Sure. Typically, we just remove those regions and don't model them. Any modeling of these regions is just going to be fantasy anyway. > >> "if distance of residue x from center is greater than some huge value >> (2-3x the predicted Rg, based on sequence length), add a bias to the >> potential for x toward the center of the protein" > > The easiest way to do that would be to add an upper bound distance restraint between each C alpha and the center of gravity of the protein. An example is at > http://salilab.org/modeller/9.11/manual/node105.html > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage
Good point. Thanks Flavio.
Daron
On May 31, 2013, at 3:54 AM, flavio seixas oivalf_nix@yahoo.com wrote:
> Hi, > > Allow me add one more option in this case. > You can use a web server that make secondary structure predictions from sequence, e.g. PsiPred (http://bioinf.cs.ucl.ac.uk/psipred/) and use the result to impose any restrictions in the protein modelling, such as alpha helices or beta-sheet. > > Regards, > > ------------------------------------- > Flavio Augusto Vicente Seixas > Laboratory of Structural Biochemistry > Department of Biochemistry > Universidade Estadual de Maringá, PR, Brazil > http://www.uem.br > > > --- On Thu, 5/30/13, Modeller Caretaker modeller-care@salilab.org wrote: > >> From: Modeller Caretaker modeller-care@salilab.org >> Subject: Re: [modeller_usage] Question about huge gaps >> To: "Daron Standley" standley@ifrec.osaka-u.ac.jp >> Cc: modeller_usage@salilab.org >> Date: Thursday, May 30, 2013, 7:35 PM >> On 05/30/2013 02:31 AM, Daron >> Standley wrote: >>> Although I'm not a very regular user of modeller, I >> believe it is well >>> known that long gaps, especially terminal gaps, look >> strange when >>> modeled using default options. >> >> Sure. Typically, we just remove those regions and don't >> model them. Any modeling of these regions is just going to >> be fantasy anyway. >> >>> "if distance of residue x from center is greater than >> some huge value >>> (2-3x the predicted Rg, based on sequence length), add >> a bias to the >>> potential for x toward the center of the protein" >> >> The easiest way to do that would be to add an upper bound >> distance restraint between each C alpha and the center of >> gravity of the protein. An example is at >> http://salilab.org/modeller/9.11/manual/node105.html >> >> Ben Webb, Modeller Caretaker >> -- modeller-care@salilab.org >> http://www.salilab.org/modeller/ >> Modeller mail list: 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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Daron Standley -
flavio seixas -
Modeller Caretaker