Re: [Chimera-users] Question about AlphaFold prediction in ChimeraX
Dear Ehsan, Next time you may want to use the address for ChimeraX, chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here, since you're using ChimeraX (not Chimera). You do not need to send this question, again, however, as I already CC'd that list. You may not be doing anything wrong -- it means that AlphaFold simply didn't predict the same thing as that paper. AlphaFold and other prediction methods are not 100% accurate, and remember also that proteins may exist in multiple conformations under different conditions, etc. Of course there are different AlphaFold settings you can try, but there is no magic recipe guaranteed to give you the best result in all situations. See the AlphaFold Options help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict> Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 16, 2026, at 8:08 AM, Ehsaneh Khodadadi via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team I am working on protein structure prediction using AlphaFold tools in ChimeraX (version 1.9 even 1.11). I am trying to model the interaction between two proteins (Tau and NDUFS3), but the predicted interaction does not match what was reported in the paper. I followed the same steps using AlphaFold in ChimeraX (tool--->structure Prediction--->AlphaFold) and past two sequences like (sequence tau, sequence NDUFS3) and then click predict, but I could not reproduce the same beta-sheet interaction. Could you please advise if there are specific settings or steps that might affect the prediction results? Thank you very much for your help. Best regards, Ehsan Khodadadi
_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/
Dear Dr. Meng Thank you very much for your explanation and for adding the ChimeraX users list. I appreciate your help. If you happen to know of any comprehensive tutorials or example PDB cases for using AlphaFold within ChimeraX, I would be very grateful if you could share them with me. I have been searching but have not found a clear step-by-step example yet. Thank you again for your guidance. Best regards, Ehsaneh ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, March 16, 2026 9:43 AM To: Ehsaneh Khodadadi <ehsaneh@stanford.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu>; chimerax-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question about AlphaFold prediction in ChimeraX Dear Ehsan, Next time you may want to use the address for ChimeraX, chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here, since you're using ChimeraX (not Chimera). You do not need to send this question, again, however, as I already CC'd that list. You may not be doing anything wrong -- it means that AlphaFold simply didn't predict the same thing as that paper. AlphaFold and other prediction methods are not 100% accurate, and remember also that proteins may exist in multiple conformations under different conditions, etc. Of course there are different AlphaFold settings you can try, but there is no magic recipe guaranteed to give you the best result in all situations. See the AlphaFold Options help: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/a... > Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 16, 2026, at 8:08 AM, Ehsaneh Khodadadi via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team I am working on protein structure prediction using AlphaFold tools in ChimeraX (version 1.9 even 1.11). I am trying to model the interaction between two proteins (Tau and NDUFS3), but the predicted interaction does not match what was reported in the paper. I followed the same steps using AlphaFold in ChimeraX (tool--->structure Prediction--->AlphaFold) and past two sequences like (sequence tau, sequence NDUFS3) and then click predict, but I could not reproduce the same beta-sheet interaction. Could you please advise if there are specific settings or steps that might affect the prediction results? Thank you very much for your help. Best regards, Ehsan Khodadadi
_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu Archives: https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/...
There are several AlphaFold-related videos in our video tutorials list, scroll down to near the bottom: <https://www.rbvi.ucsf.edu/chimerax/docs/videos/> Regards, Elaine
On Mar 16, 2026, at 9:52 AM, Ehsaneh Khodadadi via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Dr. Meng Thank you very much for your explanation and for adding the ChimeraX users list. I appreciate your help. If you happen to know of any comprehensive tutorials or example PDB cases for using AlphaFold within ChimeraX, I would be very grateful if you could share them with me. I have been searching but have not found a clear step-by-step example yet. Thank you again for your guidance. Best regards, EhsanehFrom: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, March 16, 2026 9:43 AM To: Ehsaneh Khodadadi <ehsaneh@stanford.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu>; chimerax-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question about AlphaFold prediction in ChimeraX Dear Ehsan, Next time you may want to use the address for ChimeraX, chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> CC'd here, since you're using ChimeraX (not Chimera). You do not need to send this question, again, however, as I already CC'd that list.
You may not be doing anything wrong -- it means that AlphaFold simply didn't predict the same thing as that paper. AlphaFold and other prediction methods are not 100% accurate, and remember also that proteins may exist in multiple conformations under different conditions, etc.
Of course there are different AlphaFold settings you can try, but there is no magic recipe guaranteed to give you the best result in all situations. See the AlphaFold Options help: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/a... >
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 16, 2026, at 8:08 AM, Ehsaneh Khodadadi via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team I am working on protein structure prediction using AlphaFold tools in ChimeraX (version 1.9 even 1.11). I am trying to model the interaction between two proteins (Tau and NDUFS3), but the predicted interaction does not match what was reported in the paper. I followed the same steps using AlphaFold in ChimeraX (tool--->structure Prediction--->AlphaFold) and past two sequences like (sequence tau, sequence NDUFS3) and then click predict, but I could not reproduce the same beta-sheet interaction. Could you please advise if there are specific settings or steps that might affect the prediction results? Thank you very much for your help. Best regards, Ehsan Khodadadi
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Dear Dr. Meng Excuse me, could you please let me know how to change the AlphaFold parameters to increase the chance of detecting short beta-strands? I could not find this information in the documentation. Any suggestions or recommended settings would be greatly appreciated. Best regards, Ehsaneh ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, March 16, 2026 9:58 AM To: Ehsaneh Khodadadi <ehsaneh@stanford.edu> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question about AlphaFold prediction in ChimeraX There are several AlphaFold-related videos in our video tutorials list, scroll down to near the bottom: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/docs/videos/_... > Regards, Elaine
On Mar 16, 2026, at 9:52 AM, Ehsaneh Khodadadi via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Dr. Meng Thank you very much for your explanation and for adding the ChimeraX users list. I appreciate your help. If you happen to know of any comprehensive tutorials or example PDB cases for using AlphaFold within ChimeraX, I would be very grateful if you could share them with me. I have been searching but have not found a clear step-by-step example yet. Thank you again for your guidance. Best regards, EhsanehFrom: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, March 16, 2026 9:43 AM To: Ehsaneh Khodadadi <ehsaneh@stanford.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu>; chimerax-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question about AlphaFold prediction in ChimeraX Dear Ehsan, Next time you may want to use the address for ChimeraX, chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> CC'd here, since you're using ChimeraX (not Chimera). You do not need to send this question, again, however, as I already CC'd that list.
You may not be doing anything wrong -- it means that AlphaFold simply didn't predict the same thing as that paper. AlphaFold and other prediction methods are not 100% accurate, and remember also that proteins may exist in multiple conformations under different conditions, etc.
Of course there are different AlphaFold settings you can try, but there is no magic recipe guaranteed to give you the best result in all situations. See the AlphaFold Options help: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/a... >
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 16, 2026, at 8:08 AM, Ehsaneh Khodadadi via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team I am working on protein structure prediction using AlphaFold tools in ChimeraX (version 1.9 even 1.11). I am trying to model the interaction between two proteins (Tau and NDUFS3), but the predicted interaction does not match what was reported in the paper. I followed the same steps using AlphaFold in ChimeraX (tool--->structure Prediction--->AlphaFold) and past two sequences like (sequence tau, sequence NDUFS3) and then click predict, but I could not reproduce the same beta-sheet interaction. Could you please advise if there are specific settings or steps that might affect the prediction results? Thank you very much for your help. Best regards, Ehsan Khodadadi
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It is in the AlphaFold options, as mentioned in the previous message, with help link included again here. You have to click the Options button in the AlphaFold dialog to see them. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict> Or if you are using the "alphafold predict" command, there are command options. Please see the command help for explanations: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#predict> However, it is my understanding that they usually have limited effect on the output, so it might not give anything really different than you already got. Elaine
On Mar 16, 2026, at 10:10 AM, Ehsaneh Khodadadi via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Dr. Meng Excuse me, could you please let me know how to change the AlphaFold parameters to increase the chance of detecting short beta-strands? I could not find this information in the documentation. Any suggestions or recommended settings would be greatly appreciated. Best regards, Ehsaneh
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, March 16, 2026 9:58 AM To: Ehsaneh Khodadadi <ehsaneh@stanford.edu> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question about AlphaFold prediction in ChimeraX There are several AlphaFold-related videos in our video tutorials list, scroll down to near the bottom:
<https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/docs/videos/_... >
Regards, Elaine
On Mar 16, 2026, at 9:52 AM, Ehsaneh Khodadadi via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Dr. Meng Thank you very much for your explanation and for adding the ChimeraX users list. I appreciate your help. If you happen to know of any comprehensive tutorials or example PDB cases for using AlphaFold within ChimeraX, I would be very grateful if you could share them with me. I have been searching but have not found a clear step-by-step example yet. Thank you again for your guidance. Best regards, EhsanehFrom: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, March 16, 2026 9:43 AM To: Ehsaneh Khodadadi <ehsaneh@stanford.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu>; chimerax-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question about AlphaFold prediction in ChimeraX Dear Ehsan, Next time you may want to use the address for ChimeraX, chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> CC'd here, since you're using ChimeraX (not Chimera). You do not need to send this question, again, however, as I already CC'd that list.
You may not be doing anything wrong -- it means that AlphaFold simply didn't predict the same thing as that paper. AlphaFold and other prediction methods are not 100% accurate, and remember also that proteins may exist in multiple conformations under different conditions, etc.
Of course there are different AlphaFold settings you can try, but there is no magic recipe guaranteed to give you the best result in all situations. See the AlphaFold Options help: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/a... >
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 16, 2026, at 8:08 AM, Ehsaneh Khodadadi via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Team I am working on protein structure prediction using AlphaFold tools in ChimeraX (version 1.9 even 1.11). I am trying to model the interaction between two proteins (Tau and NDUFS3), but the predicted interaction does not match what was reported in the paper. I followed the same steps using AlphaFold in ChimeraX (tool--->structure Prediction--->AlphaFold) and past two sequences like (sequence tau, sequence NDUFS3) and then click predict, but I could not reproduce the same beta-sheet interaction. Could you please advise if there are specific settings or steps that might affect the prediction results? Thank you very much for your help. Best regards, Ehsan Khodadadi
Hi Ehsaneh, AlphaFold 2 and other prediction methods in ChimeraX such as Boltz 2 and OpenFold 3 do not offer many settings that give different results. You can ask AlphaFold it to use template structures from the PDB, but it uses only templates for individual chains, so that probably won't help it find a dimerization interface. In general I find AlphaFold 2 mostly ignores the template structures if it gives a moderate to high confidence prediction. The most likely way to get alternative predictions is to run different prediction programs, for instance try Boltz prediction in ChimeraX, or OpenFold 3 prediction in ChimeraX daily builds. You can try giving those programs different random number seeds using ChimeraX boltz predict or openfold predict commands. If the predictions are low confidence that may give alternative conformations. Tom
On Mar 16, 2026, at 10:10 AM, Ehsaneh Khodadadi via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Dr. Meng Excuse me, could you please let me know how to change the AlphaFold parameters to increase the chance of detecting short beta-strands? I could not find this information in the documentation. Any suggestions or recommended settings would be greatly appreciated. Best regards, Ehsaneh
From: Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Sent: Monday, March 16, 2026 9:58 AM To: Ehsaneh Khodadadi <ehsaneh@stanford.edu <mailto:ehsaneh@stanford.edu>> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Question about AlphaFold prediction in ChimeraX
There are several AlphaFold-related videos in our video tutorials list, scroll down to near the bottom:
<https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/docs/videos/_... >
Regards, Elaine
On Mar 16, 2026, at 9:52 AM, Ehsaneh Khodadadi via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
Dear Dr. Meng Thank you very much for your explanation and for adding the ChimeraX users list. I appreciate your help. If you happen to know of any comprehensive tutorials or example PDB cases for using AlphaFold within ChimeraX, I would be very grateful if you could share them with me. I have been searching but have not found a clear step-by-step example yet. Thank you again for your guidance. Best regards, EhsanehFrom: Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Sent: Monday, March 16, 2026 9:43 AM To: Ehsaneh Khodadadi <ehsaneh@stanford.edu <mailto:ehsaneh@stanford.edu>> Cc: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>>; chimerax-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Question about AlphaFold prediction in ChimeraX Dear Ehsan, Next time you may want to use the address for ChimeraX, chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu><mailto:chimerax-users@cgl.ucsf.edu> CC'd here, since you're using ChimeraX (not Chimera). You do not need to send this question, again, however, as I already CC'd that list.
You may not be doing anything wrong -- it means that AlphaFold simply didn't predict the same thing as that paper. AlphaFold and other prediction methods are not 100% accurate, and remember also that proteins may exist in multiple conformations under different conditions, etc.
Of course there are different AlphaFold settings you can try, but there is no magic recipe guaranteed to give you the best result in all situations. See the AlphaFold Options help: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/a... >
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 16, 2026, at 8:08 AM, Ehsaneh Khodadadi via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote:
Dear ChimeraX Team I am working on protein structure prediction using AlphaFold tools in ChimeraX (version 1.9 even 1.11). I am trying to model the interaction between two proteins (Tau and NDUFS3), but the predicted interaction does not match what was reported in the paper. I followed the same steps using AlphaFold in ChimeraX (tool--->structure Prediction--->AlphaFold) and past two sequences like (sequence tau, sequence NDUFS3) and then click predict, but I could not reproduce the same beta-sheet interaction. Could you please advise if there are specific settings or steps that might affect the prediction results? Thank you very much for your help. Best regards, Ehsan Khodadadi
_______________________________________________ Chimera-users mailing list -- chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> To unsubscribe send an email to chimera-users-leave@cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> Archives: https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/...
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Hi Tom Thank you very much for the helpful explanation. I will try running Boltz and OpenFold predictions in ChimeraX with different random seeds to see whether I can obtain alternative models. I appreciate your guidance. Best regards, Ehsaneh ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Monday, March 16, 2026 2:20 PM To: Ehsaneh Khodadadi <ehsaneh@stanford.edu> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] [Chimera-users] Question about AlphaFold prediction in ChimeraX Hi Ehsaneh, AlphaFold 2 and other prediction methods in ChimeraX such as Boltz 2 and OpenFold 3 do not offer many settings that give different results. You can ask AlphaFold it to use template structures from the PDB, but it uses only templates for individual chains, so that probably won't help it find a dimerization interface. In general I find AlphaFold 2 mostly ignores the template structures if it gives a moderate to high confidence prediction. The most likely way to get alternative predictions is to run different prediction programs, for instance try Boltz prediction in ChimeraX, or OpenFold 3 prediction in ChimeraX daily builds. You can try giving those programs different random number seeds using ChimeraX boltz predict or openfold predict commands. If the predictions are low confidence that may give alternative conformations. Tom On Mar 16, 2026, at 10:10 AM, Ehsaneh Khodadadi via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Dear Dr. Meng Excuse me, could you please let me know how to change the AlphaFold parameters to increase the chance of detecting short beta-strands? I could not find this information in the documentation. Any suggestions or recommended settings would be greatly appreciated. Best regards, Ehsaneh ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> Sent: Monday, March 16, 2026 9:58 AM To: Ehsaneh Khodadadi <ehsaneh@stanford.edu<mailto:ehsaneh@stanford.edu>> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Question about AlphaFold prediction in ChimeraX There are several AlphaFold-related videos in our video tutorials list, scroll down to near the bottom: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/docs/videos/_... > Regards, Elaine
On Mar 16, 2026, at 9:52 AM, Ehsaneh Khodadadi via Chimera-users <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> wrote:
Dear Dr. Meng Thank you very much for your explanation and for adding the ChimeraX users list. I appreciate your help. If you happen to know of any comprehensive tutorials or example PDB cases for using AlphaFold within ChimeraX, I would be very grateful if you could share them with me. I have been searching but have not found a clear step-by-step example yet. Thank you again for your guidance. Best regards, EhsanehFrom: Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> Sent: Monday, March 16, 2026 9:43 AM To: Ehsaneh Khodadadi <ehsaneh@stanford.edu<mailto:ehsaneh@stanford.edu>> Cc: chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>>; chimerax-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Question about AlphaFold prediction in ChimeraX Dear Ehsan, Next time you may want to use the address for ChimeraX, chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu><mailto:chimerax-users@cgl.ucsf.edu> CC'd here, since you're using ChimeraX (not Chimera). You do not need to send this question, again, however, as I already CC'd that list.
You may not be doing anything wrong -- it means that AlphaFold simply didn't predict the same thing as that paper. AlphaFold and other prediction methods are not 100% accurate, and remember also that proteins may exist in multiple conformations under different conditions, etc.
Of course there are different AlphaFold settings you can try, but there is no magic recipe guaranteed to give you the best result in all situations. See the AlphaFold Options help: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/a... >
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 16, 2026, at 8:08 AM, Ehsaneh Khodadadi via Chimera-users <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> wrote:
Dear ChimeraX Team I am working on protein structure prediction using AlphaFold tools in ChimeraX (version 1.9 even 1.11). I am trying to model the interaction between two proteins (Tau and NDUFS3), but the predicted interaction does not match what was reported in the paper. I followed the same steps using AlphaFold in ChimeraX (tool--->structure Prediction--->AlphaFold) and past two sequences like (sequence tau, sequence NDUFS3) and then click predict, but I could not reproduce the same beta-sheet interaction. Could you please advise if there are specific settings or steps that might affect the prediction results? Thank you very much for your help. Best regards, Ehsan Khodadadi
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participants (3)
-
Ehsaneh Khodadadi -
Elaine Meng -
Tom Goddard