The Zhang Lab Message Boards

Greetings!
I am Ishita, an undergrad student. I wanted to work with peptide ligands and their interface data from the Biolip dataset, but I could find only 7315 peptides (ID: III) in the annotations.txt file of the non-redundant set. Are there more ligands that are not present in that annotations file? Because on the homepage it is given that the database currently has ~23000 peptide ligands. If yes, what is the way to download the data for all of those peptide ligands and their corresponding annotations?

TIA
Regards

Good day,

Unfortunately after two attempts of molecular modeling within two diffrerent days I have not received the homology modeled result of a FASTA protein sequences that I submitted. The estimated time was about 60 hours for each attempt. Regretfuly I forgot the accession number/code of my submitted jobs, so that I can't refer to them particularly.
Since I really appreciate I-Tasser modeling server and I used to work with it previously and never had this problem, is there a way you would tell me what my problem seems to be ?

kind regards,
Shirin Fathi

Hello
I don't know why each time i use nohup command to run ten programs in one time , i got the warning that only 3 threading programs have output, please check threading programs.
I want to know how can i resolve it, or I need to run one programs each times in local server.

start serial threading wdPPAS
pwd: couldn't find directory entry in ‘..’ with matching i-node
/mnt/nfs_storage9/zhangsiyu/local/app/I-TASSER/data/Hel_A_UBC+/wdPPAS_seq.fasta
pwd: couldn't find directory entry in ‘..’ with matching i-node
[makemat] FATAL ERROR: Unable to recover checkpoint from psitmp.chk

mv: cannot stat ‘psitmp.mtx’: No such file or directory
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 127
at c.a(c.java)
at c.main(c.java)
Illegal division by zero at /mnt/nfs_storage9/zhangsiyu/local/app/I-TASSER/data/Hel_A_UBC+/wdPPAS_seq.fasta line 348.
hostname: ubuntu-32
starting time: Sun Sep 27 10:26:54 HKT 2020
pwd: running Psi-blast .....

start serial threading wMUSTER
pwd: couldn't find directory entry in ‘..’ with matching i-node
/mnt/nfs_storage9/zhangsiyu/local/app/I-TASSER/data/Hel_A_UBC+/wMUSTER_seq.fasta
pwd: couldn't find directory entry in ‘..’ with matching i-node
hostname: ubuntu-32
starting time: Sun Sep 27 10:33:25 HKT 2020
pwd: running Psi-blast .....
running Psi-blast .....
==>2zvnC1 2kdiA 21.1378334064192 19.0763795821176
2zvnC1 2kdiA 23.17 21.95
score_flag=1
ending time: Sun Sep 27 11:21:44 HKT 2020

only 3 threading programs have output, please check threading programs

I am trying to submit a job with a specified template alignment.
The template coordinates are based off a very low resolution cryoEM map, in which we believe to have identified some domains with a known NMR structure. For the rest of the protein however, no structure is available.
Therefore, we would like to generate a model in which the location of the identified domains are specified and the rest of the model should be generated with that in mind and the PDB file has been modified accordingly and formatted according to the formatting example on the webpage.

When submitting the job, it fails with the error ‘ERROR: An error occured while reading PDB formatted threading alignment file: Residue 1 in query is M while that specified in the alignment is N.’

However, the submitted query sequence is identical to the template sequence and both start with M.
Strangely, when removing the first residue in the query (then starting with Val),the job fails with ‘ERROR: An error occured while reading PDB formatted threading alignment file: Residue 1 in query is V while that specified in the alignment is M.’

Without changing anything in the submitted PDB file, the (correct) first residue in the PDB file is identified when deleting the first residue of the query sequence?

Any ideas what could be the cause of this and how to fix it?

Cheers

I am using QUARK to draw the protein sequence which is less than 20 residues. How can I solve this issue since the system request the minimum residue is 20.

cheers

Hi,

I am modelling two proteins in TACOS. Is there a way to either specify or exclude templates for the threading of sequence A and B (before the complex threading)? I'm just having an issue with what is being applied as its in a slightly different confirmation to what I need and it is available in another template.

Thanks,
Vanessa

To whom it may concern,

I am writing to request a modelling for a protein which cannot be processed by the on-line server I-TASSER. My name is Juan Pablo Gallardo, and with my work group in the 'Immunology of Tripanosomatids Infection' Laboratory (Institute of Genetic Engineering and Molecular Biology "Dr. Héctor N. Torres" INGEBI, Buenos Aires, Argentina) we are characterizing a hypothetical protein of Trypanosoma cruzi with diagnostical potential for Chagas disease. This protein can be found in TriTrypDB with its ID: TcCLB.504087.20. Due to its size of 2983 aminoacids, it cannot be modelled entirely, only one domain per request. To our interest, a structure prediction of the complete protein would help to its characterization. We were wondering if this modelling can be perfomed by your laboratory, in a way that the size limit can be avoided. We would be beyond grateful since it would make us understand this protein better. If you agree, we can provide the aminoacidic sequence for the modelling.

Thank you for the on-line service you provide. It has helped us to comprehend this protein at its domain level and we are looking forward to extend our understanding to it entirelly.

We will be waiting for a response.

Thank you in advance,

Juan Pablo Gallardo
INGEBI
Vuelta de Obligado 2490
C1428ADN
4783-2871 int 19
Buenos Aires
Argentina

I need to study interactions between peptides that form crystals. I would like to use YASARA to dock two (or ideally more) identical peptides.
Please advise how to start!

I need to model a short 12 aa CIRCULAR peptide. It is amide cyclic, that is N-term and C-term are connected via a peptide bond. Any ideas? If 12 aa is too short I can expend it.

Dear Zhang Lab,

I have installed and am running a homology model job on a private server which i am admin on.

My question is regarding core usage. so far i have tried with the example template and also another sequence using a 1200ish protein sequence fasta.

While it seems to be running and i have ironed out errors as i have been going along, it only ever wants to use one core - which i assume you can interpret as extremely inefficient given the other 111 threads over Xenon cores which are available. I have looked over the commands and options for Torque and OpenPBS, and changed settings in an attempt to get the I-tasser suite to use more than one core per job, but so far have been unsuccessful. Just to clarify, i have used the -runstyle command and the parallel instruction. which has also not worked. i have attached screenshots of what i get under admin mode in qmgr - but please note i have hidden the server details for security.

Does I-tasser have the capability to use more than one core per sequence/job-id?

Kind Regards,

Dan

Hai,
I am a new user in I-Tasser performing ab-initio modeling for a hypothetical protein(uncharacterized one) and I have a doubt in the result page. It would be helpful if you could clarify the same
Among the top 10 threading template hits given, which among them should be selected and based on what criteria. Whether identity score should be given more weightage or the Z score? Please clarify as I am confused here.

I have been trying to use your COACH server to find the binding site of one of my compounds to my target protein. I was wondering if you could clarify some things for me. On the COACH site it only asks me for the FASTA of the protein, where do I submit my ligand structure? Thank you in advancefor your help. I look forward to hearing from you.

Is there a cross reference file of all ligands in BioLiP? I see this browse page, but it does not show other IDs such as PubChem/ChEBI ID, SMILES or InChiKey,
https://zhanglab.ccmb.med.umich.edu/BioLiP/alllig.cgi

It seems that it is not possible to download the whole list of 28641 ligands from the 955 webpages, either. Thanks.

I need to split a protein by domains for use with I-TASSER.
In THREADOM the resulting file produces several predicted domains: for instance, ‘easy’ produces 5 domains, however, in the ‘Optimization’ there are 2.
For the greatest accuracy, would I split the protein using the Predicted 'easy' type domain results, or is the 'Optimization' result information better to use?

I have submitted my job to ModRefiner tool two weeks ago. Till now i have not received the output. I have also checked my spam, but no mail is present. Last time it took approx. 2 days to receive the output.

Anyone else facing the same problem?

Hello!
I submitted a job ID: XBF1476 on Aug 05, 2020 to BindProfX server but still haven't received any result.
Can somebody help me and let me know what's going on?
Thank you!

#I want to coat a 10-mer peptide at ELISA wells for recognizing Antiserum against the native surface antigen of a virus.
1)How can I understand this 10-mer peptide has a similar 3D structure to the native surface protein? Please introduce the appropriate approach or software.
2) I wonder why when I checked the 10 top 3D, GO, and other items in the result sheet, non of them were related to the original native protein that I selected 10 aa from it?
3) I have uploaded the pbd downloaded from I-TASSER (related to a protein of SARS2) with the pbd related to 10-mer peptide ((related to the same protein of SARS2) on a server for comparing 3D structure of them, but the 10-mer sequence was not in the answer sheet of that server. I can see my 10-mer aa in the page of I-TASSER.
Please guide me

Thank you very much
Best wishes

Hi,

I think I used to see the download section for the Quark standalone. But I do not see this any longer. Would the standalone be available for download? Would C-quark be available for download in the near future too?

Greetings everyone,

I sent a job to the I-TASSER server (JOB ID: S552588) around the beginning of June and it hasn't been processed yet. I think something wrong might have happened with my inputs, because it was the first time that I suggested a template to guide the structure prediction. In all my other attempts using the default parameters my predictions followed through normally.

Thank you very much for your attention!

RNAalign

Hello,

I submitted a job on July 22, 2020 to iTasser server and I still have not received my predicted protein model. I have been checking the que on a daily basis and all jobs submitted on that day and many days after that have been processed EXCEPT for my job.

On Friday it said the job will be done in 5 hrs and now it is Tuesday and it still says the job will be done in 5 hrs. And this is a 24 amino acid sequence so a very small peptide.

Could someone please look into this and let me know what is going on?

Job ID:S557866

Hello,

according to the deepMSA paper, it is possible to use the deepMSA output for some threading algorithms during the I-TASSER run. Would there be a easy way to make I-TASSER to pick up these files?

Hi,

I hope all is well. When will the servers be available for public use? Thank you so much.

Best wishes,
Reza

Can I ask you kindly when do you expect that either of ThreaDom or ThreaDomEx will be back running, please? many thanks :)

I'm using I-Tasser to generate models for a peptide containing about 50 residues. Can we get more than 5 output models from the server?

Hi,

I am using FUpred and DeepMSA to generate a deep MSA and predict the domain boundaries. Many of the target sequences seemed to be genus/species-specific and do not have enough homologs. In one case, DeepMSA outputs a MSA of 13 similar sequences generated after hmmsearch with Nf >= 0.2, and FUpred predicted two domains 1-76 and 77-120, which I wonder would be reliable. I am running the pipeline for hundreds of sequences, and it's tricky to look at every single MSA myself. I wondered based on your experience, how much depth of the MSA you would recommend to have for reliable prediction of domain boundaries. Or in a similar sense, would there be any Nf cutoffs to filter out unreliable domain boundary predictions?

Hello first of all, thank you very much for the service that the i-tasser team provides, secondly I would like to know how much time is left for the S556898, S556886 and S558496 jobs to be completed. please help us, this work is of paramount importance for completing a survey.

good evening!
07/18/2020 I sent two proteins to the i-tasser, both with restriction but none of them has yet been modeled. I consulted by date and most of the modeling requests for this day have already been completed. I would like you to solve my problem.

the protein codes are: S556898 and S556886

user: alice.queiroz@fiocruz.br and alice.soares.queiroz03@aluno.ifce.edu.br

In addition, we also added another protein to be modeled earlier this week, but we did not receive the response from the modeling.
the id of the protein in question is S558496.
Please help us.

Hi!

I need to predict binding site for around 400 proteins (GPCRs), and I wanted to use COACH for that. Since I assume it is not feasible to run this much calculations on the web server I installed the I-TASSER suite, downloaded the database via the perl script and managed to get a sensible result by testing on one of the proteins.

However, when I run my calculations in bulk (using snakemake), the progress becomes very slow - I only managed to calculate a fraction of the results in 4 days. The program is running on a server with 128 cores and 1 Tb of RAM, and I'm running all the jobs in parallel, so 128 proteins at once. Is there anything that I could do to speed up the process? Also, should I try to reduce the number of jobs for the sake of finishing each individual job faster?

Thank you,
Ilya

my university have a cluster, in the cluster stay i-tasser and i run this program in the cluster but i have a problem with psi-blast and i don't know why
my error is:
2.1 run Psi-blast
blast cmd = /hpcfs/apps/i-tasser/5.1/blast/bin/blastpgp -b 1000 -j 3 -h 0.001 -d /hpcfs/home/lf.ariasr/itasser/proyect1/nr/nr -i protein.fasta -C psitmp.chk -Q pssm.txt > blast.out
/hpcfs/apps/i-tasser/5.1/blast/bin/blastpgp is not working properly, please check

how i can solve this?