average structure of superimposed models
Hi Elaine, I have superimposed a few highly similar models of the same protein family. They are >80% identical in sequences. I would like to find an 'average' structure as a representative model of these proteins. Can I achieve this through Chimera..? Cheers, Sum Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."
Hi Sum, Sorry, Chimera does not calculate average structures. According to the publication describing the Superpose web server, it can generate an average backbone, but only if all the structures have the same atoms (e.g. different conformations of the same protein). Superpose server: <http://wishart.biology.ualberta.ca/SuperPose/> Publication describing it: <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441615/> A long time ago I used a program named MPOSE to make a consensus CA "template" from a set of related structures, but I don't have that program anymore and don't know if it is available. It is described in this paper: T.D. Wu, S.C. Schmidler, T. Hastie, and D.L. Brutlag, "Modeling and Superposition of Multiple Protein Structures Using Affine Transformations: Analysis of the Globins" Pac Symp Biocomput 3:509 (1998). <http://psb.stanford.edu/psb-online/proceedings/psb98/abstracts/p509.html> One should be aware that an average or consensus structure can be very distorted and energetically unreasonable, depending on how it was computed. There are many issues such as whether to average coordinates for each atom or internal coordinates such as angles. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 23, 2010, at 12:00 AM, Sumitro Harjanto wrote:
Hi Elaine, I have superimposed a few highly similar models of the same protein family. They are >80% identical in sequences. I would like to find an ‘average’ structure as a representative model of these proteins. Can I achieve this through Chimera..? Cheers, Sum
And if your models have the same sequence you should try to use suppose http://structbio.vanderbilt.edu/~jsmith/suppose/ bye Marco Def. Quota "Elaine Meng" <meng@cgl.ucsf.edu>:
Hi Sum, Sorry, Chimera does not calculate average structures.
According to the publication describing the Superpose web server, it can generate an average backbone, but only if all the structures have the same atoms (e.g. different conformations of the same protein).
Superpose server: <http://wishart.biology.ualberta.ca/SuperPose/> Publication describing it: <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441615/>
A long time ago I used a program named MPOSE to make a consensus CA "template" from a set of related structures, but I don't have that program anymore and don't know if it is available. It is described in this paper:
T.D. Wu, S.C. Schmidler, T. Hastie, and D.L. Brutlag, "Modeling and Superposition of Multiple Protein Structures Using Affine Transformations: Analysis of the Globins" Pac Symp Biocomput 3:509 (1998). <http://psb.stanford.edu/psb-online/proceedings/psb98/abstracts/p509.html>
One should be aware that an average or consensus structure can be very distorted and energetically unreasonable, depending on how it was computed. There are many issues such as whether to average coordinates for each atom or internal coordinates such as angles.
Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 23, 2010, at 12:00 AM, Sumitro Harjanto wrote:
Hi Elaine, I have superimposed a few highly similar models of the same protein family. They are >80% identical in sequences. I would like to find an ‘average’ structure as a representative model of these proteins. Can I achieve this through Chimera..? Cheers, Sum
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participants (3)
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Elaine Meng -
sette＠uniroma2.it -
Sumitro Harjanto