Making oligomers from Alphafold predictions
Hi All, Apologies for the nonrelated question!! Wondering if there are any tools (can make in chimera/chimerax/Pymol) that predict or build protein oligomers based on alphfold structure. Please let me know. I will be grateful for your kind responses. Thank you Best Smith
Hi Smith, The latest ChimeraX daily builds (not the production release) include getting AlphaFold-predicted structures from the freely available AlphaFold Database. However, these are single-chain predictions only. There is an option to superimpose the single-chain predictions on an experimentally determined structure of a multimer so that the result looks like a multimer, but that is not truly the same as predicting the multimer. AlphaFold Database: <https://alphafold.ebi.ac.uk/> ChimeraX AlphaFold tool and command: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 31, 2021, at 4:28 AM, tim smith via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi All, Apologies for the nonrelated question!!
Wondering if there are any tools (can make in chimera/chimerax/Pymol) that predict or build protein oligomers based on alphfold structure. Please let me know. I will be grateful for your kind responses. Thank you
Best Smith
Hi Smith, you can use Rosetta Symmetric Docking. It's available on the ROSIE server https://rosie.rosettacommons.org/symmetric_docking -- Kevin Jude, PhD (he/him/his) Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431 On Tue, Aug 31, 2021 at 4:30 AM tim smith via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hi All, Apologies for the nonrelated question!!
Wondering if there are any tools (can make in chimera/chimerax/Pymol) that predict or build protein oligomers based on alphfold structure. Please let me know. I will be grateful for your kind responses. Thank you
Best Smith _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you, Elaine and Kevin, for your response. The Rosetta Symmetry docking is up to 400 amino acids, and mine is 800. I can't use it as it is. Wondering there is any other server for predicting symmetry. Thank you. Best Smith On Tue, Aug 31, 2021 at 7:02 PM Kevin Jude <kjude@stanford.edu> wrote:
Hi Smith, you can use Rosetta Symmetric Docking. It's available on the ROSIE server
https://rosie.rosettacommons.org/symmetric_docking
-- Kevin Jude, PhD (he/him/his) Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431
On Tue, Aug 31, 2021 at 4:30 AM tim smith via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hi All, Apologies for the nonrelated question!!
Wondering if there are any tools (can make in chimera/chimerax/Pymol) that predict or build protein oligomers based on alphfold structure. Please let me know. I will be grateful for your kind responses. Thank you
Best Smith _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Smith, Do you know the symmetry of the oligomer you are trying to make? Is it just a matter of applying positions that you already know? Or do you need some computational protein-protein docking to figure it out (a vastly harder problem)? If you know the symmetry you want the Chimera and ChimeraX sym command can place copies of a structure using standard symmetries or a list of position matrices (rotation + translation). tom
On Sep 1, 2021, at 1:29 AM, tim smith via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Thank you, Elaine and Kevin, for your response. The Rosetta Symmetry docking is up to 400 amino acids, and mine is 800. I can't use it as it is. Wondering there is any other server for predicting symmetry.
Thank you.
Best Smith
On Tue, Aug 31, 2021 at 7:02 PM Kevin Jude <kjude@stanford.edu <mailto:kjude@stanford.edu>> wrote: Hi Smith, you can use Rosetta Symmetric Docking. It's available on the ROSIE server
https://rosie.rosettacommons.org/symmetric_docking <https://rosie.rosettacommons.org/symmetric_docking> -- Kevin Jude, PhD (he/him/his) Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431 <tel:%28650%29%20723-6431> On Tue, Aug 31, 2021 at 4:30 AM tim smith via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: Hi All, Apologies for the nonrelated question!!
Wondering if there are any tools (can make in chimera/chimerax/Pymol) that predict or build protein oligomers based on alphfold structure. Please let me know. I will be grateful for your kind responses. Thank you
Best Smith _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
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Elaine Meng -
Kevin Jude -
tim smith -
Tom Goddard