Can FDpred standalone version work with proteins whose length > 1,500 aa?

This forum is shown on the index page along with all topics.

Moderator: robpearc

chainorato
Posts: 4
Joined: Sat Jun 19, 2021 4:54 pm

Can FDpred standalone version work with proteins whose length > 1,500 aa?

Post by chainorato »

Hi, I have a protein whose length > 1,500 aa that I want to predict a 3D structure.
So I used the online ThreaDomEx to predict the protein boundary before submitting it to DEMO.

However, it seems ThreaDomEx does not work anymore.
I found that FDpred on the online server cannot be used for proteins whose length > 1,500 aa.

I would like to know that can FDpred standalone version work with proteins whose length > 1,500 aa or not.
If not, how can I work with it instead?

Thank you in advance!
xiaogenz
Posts: 92
Joined: Sun Apr 25, 2021 12:02 am

Re: Can FDpred standalone version work with proteins whose length > 1,500 aa?

Post by xiaogenz »

chainorato wrote: Sun Jun 20, 2021 3:35 am Hi, I have a protein whose length > 1,500 aa that I want to predict a 3D structure.
So I used the online ThreaDomEx to predict the protein boundary before submitting it to DEMO.

However, it seems ThreaDomEx does not work anymore.
I found that FDpred on the online server cannot be used for proteins whose length > 1,500 aa.

I would like to know that can FDpred standalone version work with proteins whose length > 1,500 aa or not.
If not, how can I work with it instead?

Thank you in advance!
You can try to use our new developed server https://zhanglab.dcmb.med.umich.edu/I-TASSER-MDA/ for automated multi-domain protein structure prediction. But the server is still testing.
chainorato
Posts: 4
Joined: Sat Jun 19, 2021 4:54 pm

Re: Can FDpred standalone version work with proteins whose length > 1,500 aa?

Post by chainorato »

Thank you very much for your prompt response!
I've submitted it through I-TASSER-MDA and it works.
chainorato
Posts: 4
Joined: Sat Jun 19, 2021 4:54 pm

Re: Can FDpred standalone version work with proteins whose length > 1,500 aa?

Post by chainorato »

Hi, Could you please check the status of the I-TASSER-MDA job ITM226 for me?
The waiting panel stated that "it will take about 72 hours to complete (job submitted at: Sun Jun 20 03:07:50 EDT 2021)", but there is still nothing in return.
xiaogenz
Posts: 92
Joined: Sun Apr 25, 2021 12:02 am

Re: Can FDpred standalone version work with proteins whose length > 1,500 aa?

Post by xiaogenz »

The job is still in processing. As you select to predict the protein function, the required time are doubled.
jlspzw
Posts: 36
Joined: Tue May 04, 2021 5:04 pm

Re: Can FDpred standalone version work with proteins whose length > 1,500 aa?

Post by jlspzw »

FUpred can handle the protein with large 1,500AA by standalone version, if you do not want to wait, you can try it by your computer.
chainorato
Posts: 4
Joined: Sat Jun 19, 2021 4:54 pm

Re: Can FDpred standalone version work with proteins whose length > 1,500 aa?

Post by chainorato »

Hi again, I finally got an e-mail that the job id ITM226 has been finished on the I-TASSER-MDA server.
The e-mail stated that I can also see and download the modeling structure of your job in the link it provided.

However, I just found the waiting message
The protein with name "XXX" (1898 AAs) has been successfully submitted and is being processed......

Could you please help me to get access to the modeling result?
Post Reply