[chimerax-users] [EXT] Re: missing or invalid sequences

Thu Jan 19 11:03:13 PST 2023

Hi Junyi,
AlphaFold did not predict whether it would be a homodimer or not: your input told it to try to predict a homodimer.  However, from the image you can see the lack of contacting folded structure, and the pLDDT coloring and predicted aligned error show low confidence, which all suggest it is unlikely.

However, you would need to apply your common sense and research whether there is any other biochemical evidence that it does form a multimer with itself or some other proteins.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 19, 2023, at 10:52 AM, Liang, Junyi via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Meng,
> 
> Below is from alphafold21_predict_colab.ipynb. Does this mean the two proteins is predicated to form a dimer(homo-dimer)?
> 
> Best,
> 
> Junyi
> <image.png>
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Thursday, January 19, 2023 1:00 PM
> To: Liang, Junyi <LIANGJ3 at ccf.org>
> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] [EXT] Re: missing or invalid sequences
>  
> CAUTION CYBER RISK: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender, expected to receive this content and trust that it’s safe. If you determine that the email isn’t from a trusted source, you can delete the email, submit it via the BlueFish button in Outlook for investigation or forward the email as an attachment to phishtanktriage at ccf.org if you don’t have the Bluefish button or are on a mobile device.
> 
> Hi Junyi,
> It works fine for me in ChimeraX 1.5 AlphaFold Predict if I paste the following: 
> 
> MPDPLFSAVQGKDEILHKALCFCPWLGKGGMEPLRLLILLFVTELSGAHNTTVFQGVAGQSLQVSCPYDS
> MKHWGRRKAWCRQLGEKGPCQRVVSTHNLWLLSFLRRWNGSTAITDDTLGGTLTITLRNLQPHDAGLYQC
> QSLHGSEADTLRKVLVEVLADPLDHRDAGDLWFPGESESFEDAHVEHSISRSLLEGEIPFPPTSILLLLA
> CIFLIKILAASALWAAAWHGQKPGTHPPSELDCGHDPGYQLQTLPGLRDT,
> MPDPLFSAVQGKDEILHKALCFCPWLGKGGMEPLRLLILLFVTELSGAHNTTVFQGVAGQSLQVSCPYDS
> MKHWGRRKAWCRQLGEKGPCQRVVSTHNLWLLSFLRRWNGSTAITDDTLGGTLTITLRNLQPHDAGLYQC
> QSLHGSEADTLRKVLVEVLADPLDHRDAGDLWFPGESESFEDAHVEHSISRSLLEGEIPFPPTSILLLLA
> CIFLIKILAASALWAAAWHGQKPGTHPPSELDCGHDPGYQLQTLPGLRDT
> 
> I don't know what was wrong in your case. Remember it has to be plain text, without any quotation marks or other special characters.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Jan 19, 2023, at 9:04 AM, Liang, Junyi via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> > 
> > Hello Elaine,
> > 
> > It's nice to hear from you. I guess I input the sequence in a correct way as I tried to input the sequence the same way as in this video https://www.youtube.com/watch?v=6lXeCPuTePs 
> > 
> > Running AlphaFold to Predict Protein Complexes from ChimeraX
> > How to predict the structure of a photoreaction center complex of 3 proteins from ChimeraX using AlphaFold-Multimer. Requires a ChimeraX daily build newer than December 2, 2021 or version 1.4. It is not in ChimeraX version 1.3. Web page describing steps https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html
> > www.youtube.com
> > Below is a screenshot of interface. I would like to do a protein-protein interaction predication.
> > <image.png>
> > Best,
> > 
> > Junyi
> > From: Elaine Meng <meng at cgl.ucsf.edu>
> > Sent: Thursday, January 19, 2023 11:34 AM
> > To: Liang, Junyi <LIANGJ3 at ccf.org>
> > Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> > Subject: [EXT] Re: [chimerax-users] missing or invalid sequences
> > 
> > CAUTION CYBER RISK: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender, expected to receive this content and trust that it’s safe. If you determine that the email isn’t from a trusted source, you can delete the email, submit it via the BlueFish button in Outlook for investigation or forward the email as an attachment to phishtanktriage at ccf.org if you don’t have the Bluefish button or are on a mobile device.
> > 
> > Without the details of what you did, I can only guess that somehow you did not enter the sequences correctly. They should be plain text, with only a comma between sequences of different proteins.
> > 
> > see AlphaFold predict help:
> > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict>
> > 
> > To say anything more informative, we would need to see exactly what you pasted into the sequence area, and what options you chose in the input dialog.
> > 
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D. 
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> > 
> > 
> > > On Jan 19, 2023, at 7:27 AM, Liang, Junyi via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> > > 
> > > I would like to predicate interaction between two proteins, and tried chimerax version 1.5 after noticing a youtube video https://www.youtube.com/watch?v=6lXeCPuTePs.
> > > 
> > > Running AlphaFold to Predict Protein Complexes from ChimeraX
> > > How to predict the structure of a photoreaction center complex of 3 proteins from ChimeraX using AlphaFold-Multimer. Requires a ChimeraX daily build newer than December 2, 2021 or version 1.4. It is not in ChimeraX version 1.3. Web page describing steps https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html
> > > www.youtube.com
> > > I input the two protein sequences in same way as shown in the video and hit predict. But your software says "missing or invalid sequences". How come?
> > > 
> 
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