Using ChimeraX to predict protein-protein interaction/binding via Alphafold.
Dear Sir/Mdm,
Sorry to disturb you with regards to this matter, as I am unable to find any resources online, or on your YouTube channel to solve my problem. I am William, a medical student at King's College London, UK, who have been using your software, ChimeraX, for the past few months to elucidate possible protein structure for one of the protein I am currently studying. I have faced a problem with predicting a protein interaction between a heterodimer (6z1n) and a novel protein that I am studying now. When I loaded both pdbs, I am unable to run the alphafold via the command:
alphafold predict #1 (where #1 is 6z1n and #2 is my protein of interest)
Hence, how can I load the pdb of 6z1n (the heterodimer) and the sequence of the protein of interest to predict what is the possible interaction between the 2, instead of putting all 3 monomers as a sequence and for Alphafold to repredict the interactions between the2 monomers within 6z1n instead?
Thank you very much and sorry to disturb you!
Sincerely Yours, William Tan
Hi William, The "&" is wrong -- that symbol is for intersection, and the intersection between the two different models is nothing (none of the atoms are in both #1 and #2 at the same time). I.e. to specify both models together try #1,2 instead:
alphafold predict #1,2
https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#combinations
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 5, 2022, at 6:44 AM, Tan, Wei Ren via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Sir/Mdm,
Sorry to disturb you with regards to this matter, as I am unable to find any resources online, or on your YouTube channel to solve my problem. I am William, a medical student at King’s College London, UK, who have been using your software, ChimeraX, for the past few months to elucidate possible protein structure for one of the protein I am currently studying. I have faced a problem with predicting a protein interaction between a heterodimer (6z1n) and a novel protein that I am studying now. When I loaded both pdbs, I am unable to run the alphafold via the command:
alphafold predict #1 (where #1 is 6z1n and #2 is my protein of interest)
Hence, how can I load the pdb of 6z1n (the heterodimer) and the sequence of the protein of interest to predict what is the possible interaction between the 2, instead of putting all 3 monomers as a sequence and for Alphafold to repredict the interactions between the2 monomers within 6z1n instead?
Thank you very much and sorry to disturb you!
Sincerely Yours, William Tan
Dear Elaine,
Thank you very much for your quick response. I have actually tried the #1,#2 but the code does not recognize the protein sequence as a sequence.
Missing or invalid "sequences" argument. Sequence argument #1 is not a chain-specifier, alignment ID, UniProt ID or sequence character.
I downloaded the pdb from RCSB.
May I know what other methods can I use to perform the task?
Thank you very much.
Sincerely Yours, William Tan
________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Wednesday, 5 October 2022, 4:55 pm To: Tan, Wei Ren Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Using ChimeraX to predict protein-protein interaction/binding via Alphafold.
[You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
Hi William, The "&" is wrong -- that symbol is for intersection, and the intersection between the two different models is nothing (none of the atoms are in both #1 and #2 at the same time). I.e. to specify both models together try #1,2 instead:
alphafold predict #1,2
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 5, 2022, at 6:44 AM, Tan, Wei Ren via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Sir/Mdm,
Sorry to disturb you with regards to this matter, as I am unable to find any resources online, or on your YouTube channel to solve my problem. I am William, a medical student at King’s College London, UK, who have been using your software, ChimeraX, for the past few months to elucidate possible protein structure for one of the protein I am currently studying. I have faced a problem with predicting a protein interaction between a heterodimer (6z1n) and a novel protein that I am studying now. When I loaded both pdbs, I am unable to run the alphafold via the command:
alphafold predict #1 (where #1 is 6z1n and #2 is my protein of interest)
Hence, how can I load the pdb of 6z1n (the heterodimer) and the sequence of the protein of interest to predict what is the possible interaction between the 2, instead of putting all 3 monomers as a sequence and for Alphafold to repredict the interactions between the2 monomers within 6z1n instead?
Thank you very much and sorry to disturb you!
Sincerely Yours, William Tan
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It is #1,2 -- not #1,#2. Before I sent the previous message, tried the first one myself with alphafold predict and it worked.
Elaine
On Oct 5, 2022, at 9:03 AM, Tan, Wei Ren via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Elaine,
Thank you very much for your quick response. I have actually tried the #1,#2 but the code does not recognize the protein sequence as a sequence.
Missing or invalid "sequences" argument. Sequence argument #1 is not a chain-specifier, alignment ID, UniProt ID or sequence character.
I downloaded the pdb from RCSB.
May I know what other methods can I use to perform the task?
Thank you very much.
Sincerely Yours, William Tan
From: Elaine Meng meng@cgl.ucsf.edu Sent: Wednesday, 5 October 2022, 4:55 pm To: Tan, Wei Ren Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Using ChimeraX to predict protein-protein interaction/binding via Alphafold.
[You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
Hi William, The "&" is wrong -- that symbol is for intersection, and the intersection between the two different models is nothing (none of the atoms are in both #1 and #2 at the same time). I.e. to specify both models together try #1,2 instead:
alphafold predict #1,2
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 5, 2022, at 6:44 AM, Tan, Wei Ren via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Sir/Mdm,
Sorry to disturb you with regards to this matter, as I am unable to find any resources online, or on your YouTube channel to solve my problem. I am William, a medical student at King’s College London, UK, who have been using your software, ChimeraX, for the past few months to elucidate possible protein structure for one of the protein I am currently studying. I have faced a problem with predicting a protein interaction between a heterodimer (6z1n) and a novel protein that I am studying now. When I loaded both pdbs, I am unable to run the alphafold via the command:
alphafold predict #1 (where #1 is 6z1n and #2 is my protein of interest)
Hence, how can I load the pdb of 6z1n (the heterodimer) and the sequence of the protein of interest to predict what is the possible interaction between the 2, instead of putting all 3 monomers as a sequence and for Alphafold to repredict the interactions between the2 monomers within 6z1n instead?
Thank you very much and sorry to disturb you!
Sincerely Yours, William Tan
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Using the command "alphafold predict #1,2" is handing the 3 monomer sequences (two from the #1 dimer, and one from the #2 monomer) to Alphafold and making a prediction for the interaction of those 3 monomers. It is not using the PDB models of the dimer and monomer. AlphaFold does not dock existing models, it makes predictions from sequences.
Tom
On Oct 5, 2022, at 6:44 AM, Tan, Wei Ren via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hence, how can I load the pdb of 6z1n (the heterodimer) and the sequence of the protein of interest to predict what is the possible interaction between the 2, instead of putting all 3 monomers as a sequence and for Alphafold to repredict the interactions between the2 monomers within 6z1n instead?
participants (3)
-
Elaine Meng -
Tan, Wei Ren -
Tom Goddard