The Zhang Lab Message Boards

MY Objective: Predict the Binding sites or is the number “one” in the binary sequence?

Each protein has three characteristics was obtained from the BioLip :
Protein name, Alphabetical sequence and Binary sequence
How do I find out that the letter R In alphabetical sequence that
Is equivalent to the number one in the binary sequence?
In BIOLIP ,there are 2 ways
Solution one is:
>1avpA

SANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRNYLGGFALSVAHGRKAHHYTIERELNGTYAIAGGRTHASPADLCHYHSQESDGLVCLLKKPFNRPQGVQPKTGPFEDLKENLIREYVKQTWNLQGQALEQAIISQKPQLEKLIATTAHEKMPWFHGKISREESEQIVLIGSKTNGKFLIRARDNNGSYALCLLHEGKVLHYRIDKDKTGKLSIPEGKKFDTLWQLVEHYSYKADGLLRVLTVPCQKI

00000000000001100000000000000000010000000000000000000011100000000001100000000000000000000100000000000000000000000000000000000000000000000000000000000000000000000000001000000000000000000010100000000000000001111000000000011101000000000000001011000000000000
The amino acid R is in position 14

Solution two is: this Solution is kind of benchmark

>1avpA

R22 E23 R42 H63 Y64 T65 I76 A77 G98 R175 R195 R197 L214 H215 Y216 R217 I228 P229 E230 K232 K247 D249 G250

The amino acid R is in position 22

1-Please explain this difference ?
2-What is the relationship of the number one in a binary sequence with the corresponding amino acid in the alphabetical sequence, so How can I find that the amino acid R in the alphabetical sequence is equivalent to the number one in the binary sequence?

Greetings,

I am waiting for several weeks the results for the job PD103313. Is it still running?

Sincerely,

Hi,

I had started an I-TASSER run (Job ID S500152) for my protein on 20th October and it has not finished.

I appreciate that the server is undergoing maintenance and this may have contributed to the delay. There may be another reason as well.

Please could you report on the progress of the run as I am unaware of any log file I can access to get specific details on it. Perhaps the run may need to be cancelled or resubmitted again.

Thank you for your assistance.

Regards,

Abbas

I have submitted two protein sequences trying to know predicted both Ligand binding site and active site residues. the two proteis are king of related but are very different in terms they activity based on our work. One of them (pPLAIIIa with job ID S501686) had only Ligand binding sites and nothing on the enzyme active site residues. The other one which is pPLAIIa with a job ID S502997 showed both Ligand binding site and active site residues. The folding looks almost the same, my question is why pPLAIIIa (from lab work has almost no activity when expressed in bacteria) did not show enzyme active site residues? what does this prediction results actually mean? any idea why a protein might not predict the enzyme active site? Could it be like it needs another protein to be active? I am just wondering

Bellow are the job IDs for the two protein results from your lab. Any comments about this issue please let me know since I am not an expert in protein predictions.
ID S501686
ID S502997

Thank you so much for the great work your are doing.

Hi,

> I am YongLiang Jiang from University of Science and Technology of
> China. Recently I used your online server I-TASSER-MR to solve the
> structure of a complex (two components) by molecular replacement. Can
> I put the two protein sequences together and let the program to search
> for the two comonents in one run? Alternatively, I search for the two
> components separately and merge the results together? What do you
> suggest me to do?
>
> Thank you very much for your help!

I have submitted a job in ITASSER webserver 2 days ago (Job ID:S503006), but result not arrived yet. How long it is going to take?

Greetings!
Does I-TASSER standalone version 5.1 support multi-domains protein as input or I should model each domain independently?

Thanks

Greetings!

I am Bennett Henzeler, working as a Research Intern in the area of HIV infection at ICMR-NIRT, India. Recently we used QUARK and I-Tasser Modeller for prediction of highly similar sequences (Aligned them and verified using MEGA and CLUSTAL W). But the models predicted were totally different (we tried to superimpose them using pymol and the RMSD was 17). We have 44 such similar sequences, out of which 5 were done with QUARK and I-Tasser. The difference in the models has put a pause on our work. We were planning to predict the function of the protein based on these structures.

The secondary structures predicted by both the program are same but the tertiary structures vary. So we have a doubt whether the folding may differ from one to another even with sequence high homology and similar secondary structures. The below file attached m1asp1ref is I-Tasser and m1asp1 is Quark

For further assistance all the sequences uploaded from mail id's ending with nirt.res.in are from our project centre, you can look into those structures predicted

Regards
Bennett Henzeler
benz4166henzeler@gmail.com
C/o Ashokkumar Manickam
ICMR-NIRT

Hi,

I ran the BindProfX standalone and get three scores, listed in
FoldXScore.txt, XProfScore.txt and result.txt.

How is result.txt derived from FoldXScore.txt and XProfScore.txt? It does not seem to match the 0.9/0.4 weight ratio mentioned for evoscore and foldx score as mentioned in the article.

Thank You!

https://zhanglab.ccmb.med.umich.edu/ResPRE/

I saw the download link on this website. Clicking in is the data of Training set of ResPRE and
Test set of ResPRE.
But the data in this link such as d102ma_、d351ca_...
My question is:How to download a sequence to them d102ma_?
Thank you

I have submitted the Job PD103313 an it did not returned yet...

Hi,

Is it possible to use BindProfx on a multimer with more than two chains?

Thank you!

How long should you let a job run before it's considered a run away job that should be killed? For reference the proteins I am interested in are about 300 amino acids.

Dear Colleagues,

I need the source code or executable of QUARK force field which will provide the values of all 11 terms present in the force field. Please help me in this regard.

Regards
-Abantika

Greetings,

I need to design a 3D small pepitide that could mimetize the interaction of a homodimeric protein that performs an allosteric switch binding in a heterodimeric receptor membrane-protein. I docked the protein to the receptor and submitted the complex (PDB file) to EvoDesign server somo weeks ago and I am waiting the job finiches the calculation. I am a completely beginner in "De novo" design, and that is my first time using the EvoDesign tool, so any clues how to proceed and to analyze my results are very welcome!

Sincerely

Dear Administrator,

I tried using I-TASSER (v5;1) and kept recieving the same error message, attached below. Also, I've attached the folder and the I-TASSER files and my imput file. Would you please let me know what I could do to fix this problem please? Thank you in advance.

Your setting for running I-TASSER is:
-pkgdir = /home/vspires/I-TASSER5.1/I-TASSER5.1
-libdir = /home/db/I-TASSER5.1/libdir
-java_home = /usr
-seqname = NOME
-datadir = /home/vspires/I-TASSER5.1/I-TASSER5.1/example
-outdir = /home/vspires/I-TASSER5.1/I-TASSER5.1/example
-runstyle = gnuparallel
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 10
-light = false
-hours = 50
-LBS = false
-EC = false
-GO = false

1. make seq.txt and rmsinp
Your protein contains 24 residues:
> NOME
RFASTSSSSDGYGQYGDYHAHPDV
2.1 run Psi-blast
[blastpgp] WARNING: [000.000] posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix

2.2 Predict secondary structure with PSSpred...
2.3 Predict solvent accessibility...
2.4 run pairmod
2.4.1 Use all templates
submit threading jobs first and run pair during threading
3.1 do threading
start gnuparallel threading PPAS
start gnuparallel threading dPPAS
start gnuparallel threading dPPAS2
start gnuparallel threading Env-PPAS
start gnuparallel threading MUSTER
start gnuparallel threading wPPAS
start gnuparallel threading wdPPAS
start gnuparallel threading wMUSTER
Illegal division by zero at /home/vspires/I-TASSER5.1/I-TASSER5.1/example/PPAS_NOME line 354.
Illegal division by zero at /home/vspires/I-TASSER5.1/I-TASSER5.1/example/dPPAS_NOME line 356.
Illegal division by zero at /home/vspires/I-TASSER5.1/I-TASSER5.1/example/dPPAS2_NOME line 355.
Illegal division by zero at /home/vspires/I-TASSER5.1/I-TASSER5.1/example/Env-PPAS_NOME line 352.
ERROR: fscanf failed to read model

hi,

I've been using i-Tasser "TM-align" to align two crystal structures, let's say CS-A and CS-B. This worked very well and the alignment score based on CS-A was 0.86 and for CS-B was 0.73.

Protein B is a hexamer made up of 3 dimers, and the crystal structure of B was solved as a hexamer.

Protein A is a dimer, and was crystallized as a dimer. Based on the high level of structural similarity, I wanted to test if protein A could also form a hexamer made up of 3 dimers.

Is there a mechanism to model protein A into the protein B hexamer? Is this something that should be done using different software such as Schrodinger? (and if so, could you recommend a website with instructions?).

Many thanks for ideas.

Hello, I have installed I-TASSER 5.1 on one of our linux machines (running Ubuntu 16.04) and have tried a test run using a short sequence, as advised.

However, I am getting this error:

(...)
7 run COACH to predict function: Ligand-binding site,EC number,GO terms...
/data/2TBssd1/usr/local/i-tasser/I-TASSER5.1/I-TASSERmod/runCOACH.pl -pkgdir /data/2TBssd1/usr/local/i-tasser/I-TASSER5.1 -libdir /data/2TBssd1/usr/local/i-tasser/ITLIB -runstyle serial -protname seq.fasta -model model1.pdb -datadir /data/2TBssd1/usr/local/i-tasser/test -homoflag real -idcut 1 -LBS true -EC true -GO true
cp: cannot stat '/data/2TBssd1/usr/local/i-tasser/ITLIB/PDB//3n96A.pdb': No such file or directory
cp: cannot stat '/data/2TBssd1/usr/local/i-tasser/ITLIB/GO/MTX/3n96A.mtx': No such file or directory
cp: cannot stat '/data/2TBssd1/usr/local/i-tasser/ITLIB/GO/PRF/3n96A.prf': No such file or directory
At line 174 of file PRTMalign.f
Fortran runtime error: No such file or directory
Argument "74A" isn't numeric in sprintf at /data/2TBssd1/usr/local/i-tasser/test/model1/cofactor/CF_seq.fasta_model1.pl line 2230, line 221.
Argument "74A" isn't numeric in sprintf at /data/2TBssd1/usr/local/i-tasser/test/model1/cofactor/CF_seq.fasta_model1.pl line 2230, line 222.
cp: cannot stat '/data/2TBssd1/usr/local/i-tasser/test/model1/tmsite/tms_*.pdb': No such file or directory
cat: tms_1uzjA_BS01_CA.pdb: No such file or directory
cat: tms_5ky8B_BS01_BGC.pdb: No such file or directory
cat: tms_5vygB_BS01_GXX.pdb: No such file or directory

...and indeed, the 3n96A.* files mentioned above appear to be missing from the libraries, which I just downloaded yesterday.

How to fix this problem?

Thanks and best regards,

Luca

Dear colleagues,

I am running a test of my local version of I-TASSER-5.1. I have submitted jobs for several proteins both on local package and on web-server. However, I have found out that the final models differ sufficiently (not as rotamers of side-chains). I have updated the ITLIB last week, and downloaded the full 89 GB of the libraries. Where can the problem come from? I am running the gnu-parallel calculations.

Best regards,
Dmitrii

Dear Zhang lab,

I would like to suggest/request that you add the option to input a user-generated MSA in the LOMETS2 server (it would, of course, also be useful in many of your other servers - explanation below).

Your new DeepMSA pipeline is well thought out, however it prevents users from including non-redundant sequences absent from UniProt (UniClust/UniRef) and Metaclust.

To clarify:

1. There are currently many genome assemblies whose predicted proteome is not yet included in any major public database (UniProt or NCBI). These proteomes are only available in specialized genomic databases (e.g. TriTrypDB for kinetoplastids), lab group websites and/or data repositories like Dryad.

2. Likewise, there are thousands of published transcriptome assemblies whose predicted protein sequences are, again, made available only in specific databases or data repositories, outside the realm of UniProt or NCBI. Particularly important examples include the Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) and the 1000 Plants Project (1kP). Transcriptome datasets are all the more relevant because in many cases, particularly for protist species without a sequenced genome, they are our only window into a given species proteome.

3. Metaclust is great, but unfortunately misses other metagenomics/metatranscriptomics datasets, like the ones included in the Soil Reference Catalog (SRC) and Marine Eukaryotic Reference Catalog (MERC), also generated in Söding's lab.

Rich, manually curated MSAs that include sequences from all available sources, as detailed above, have the potential to be much more informative for LOMETS (and other servers from your lab) than the ones DeepMSA is currently able to generate.

Is it possible to model dimer in SAXSTER? when i upload two fasta sequences combined the results are not satisfactory. It would be great if one could say force p2 symmetry.

And, is it possible to implement pdb file for a template? I have a pdb that is not yet online, but there is no option for upload.

Best regards,

Jacek

Hi, just wonder what's the improved performance with the advance options "remove templates sharing >30% sequence identity with target" for I-TASSER. Thanks.

Dear friends,

I am new to I-tasser, and have run de novo structure prediciton on a 382 long proteins sequence. Could you please guide me to where can I find on how can I assess the results from I-tasser? The command line I used is:

/I-TASSER5.1/I-TASSERmod/runI-TASSER.pl -pkgdir /softwares/itasser/I-TASSER5.1 -libdir /softwares/itasser/ITLIB -seqname sequence -datadir itasser-local -runstyle gnuparallel -homoflag benchmark -LBS true -java_home /usr -traj -light -outdir itasser-local/ &> itasser-log.log &

Thanks!

I see the method to suggest one PDB file as a user-derived template. If I would like to specify two different files to be templates for different regions of the model, how would I indicate which region of the model should be informed by which template?

the end user agreement that I could see specifies license terms for download of the I-TASSER suite. I do not wish to download the software suite, I would like to use the on-line service of I-TASSER: If i use the on line I-TASSER server to generate models, are there limits of the models? (such as with respect to commercial use)
thanks

i want to analyse the protein interaction of my protein of interest and i need to have an protein structure, for this i used i-Tasser, i want to know that do i need to optimized the structure further or the model (structure) generated is already optimized through i-tasser server?

Hello,

I'd like to use IonCom on a HPC infrastructure.

To do this, I'm copying the I-TASSER library to a compute node, but it's very large.

Is not IonCon only relying on one/few subfolder of the library?

If so:

- which ones?

and

- is it okay to only copy these one/few I-TASSER library subfolders to run IonCom onto?

Thanks!

Franck

An error has occured for target S0992A-S0992B
SPRING job has failed

Hello to everyone,

this might be a very naive question but is there a way of changing some graphic parameters for producing a good quality output figure from STRUM? We have done a STRUM analysis but the output figure resolution is quite low. Is there a way of changing that? Alternatively, given the output mutability file, is there a package in R where this file could be used as input in order to get the desired figure in high resolution?

Thanks for any help!!!

Dimitrios

Hello,

I am running mPSSpreds.pl from I-TASSER5.1 package. It works fine for most of the sequences I am testing but fail with some, for example it fails with this sequence:
CCQIVPQCCXWN (X represents a modified amino acid that I want to get excluded)

It fails with:
Illegal division by zero at ../../mPSSpred.pl line 417.

The same happens with sequence XKPWPPGHHIPP for example.

Thanks a lot for your help