Online Services

●I-TASSER ●I-TASSER-MTD ●C-I-TASSER ●CR-I-TASSER ●QUARK ●C-QUARK ●LOMETS ●MUSTER ●CEthreader ●SEGMER ●DeepFold ●DeepFoldRNA ●FoldDesign ●COFACTOR ●COACH ●MetaGO ●TripletGO ●IonCom ●FG-MD ●ModRefiner ●REMO ●DEMO ●DEMO-EM ●SPRING ●COTH ●Threpp ●PEPPI ●BSpred ●ANGLOR ●EDock ●BSP-SLIM ●SAXSTER ●FUpred ●ThreaDom ●ThreaDomEx ●EvoDesign ●BindProf ●BindProfX ●SSIPe ●GPCR-I-TASSER ●MAGELLAN ●ResQ ●STRUM ●DAMpred

●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

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Frequently Asked Questions (FAQs)

• 1. Why did I fail to receive the password after registration?
• 2. Why does my password not work for the I-TASSER server?
• 3. Why does my password not work for the I-TASSER Suite, I-TASSER Forum, or QUARK server?
• 4. How can I predict the structure of a protein with >1,500 residues?
• 5. How can I run I-TASSER suite on Mac, Windows or 32-bit Linux?
• 6. Why my SAXSTER prediction did not return any result?
• 7. How can I use I-TASSER models to predict the effect of mutations on the overall topology?
• 8. How do I report bugs for web services and softwares from Yang Zhang lab?
• 9. What are the 'top 10 templates used by I-TASSER' in the Result page?
• 10. What is the 'top 5 models predicted by I-TASSER' in the Result page?
• 11. What are 'Proteins structurally close to the target in the PDB' in the Result page?
• 12. What is C-score in the Result page?
• 13. What is TM-score in the Result page?
• 14. What is difference and relationship between C-score and TM-score?
• 15. Why some lower-rank models have higher C-score in the Result page?
• 16. Why do I-TASSER models have worse ramachandran plot than other structure prediction program?
• 17. Why do I received only one model instead of five models?
• 18. What molecular graphic software should be used to visualize I-TASSER structure models?

Your may find answer to other questions at the Service System Discussion Board.


1, Why did I fail receive the password for I-TASSER Server after my registration?

A confirmation email with password will be sent to you, after you register your email in the I-TASSER server. But since the confirmation emails were sent out automatically by computer, it is possible that the confirmation email was filtered out by your email security system. So it is wise to check your junk E-mail folders, if you did not receive a confirmation email in your inbox in time. If you found that you did not receive the confirmation email one hour after you correctly submitted your registration information, please contact yangzhanglab@umich.edu and let us know the email that you registered. We can resend the registration information to you, manually.

2. Why does my password not work for I-TASSER Server?

If you copy and paste your password from the confirmation email, please remember not to include any space before and after the password. For example, if your password is IT_8abcd, please make sure that you did not type in " IT_8abcd" or "IT_8abcd ", which is the mistake most frequently made by new users.

3. Why does my password not work for I-TASSER Suite, I-TASSER Forum, or QUARK server?

Are you using the password obtained from I-TASSER server to download I-TASSER Suite? The I-TASSER Server, I-TASSER Suite, I-TASSER Forum, and QUARK webserver are independent systems. You need to register them separately for different passwords.

4. How can I predict the structure of a protein with >1,500 residues?

(Short answer) No, you can not. The I-TASSER server only accepts for sequence below 1,500 residues.

(Long answer) The server version of I-TASSER has not been optimized for multi-domain proteins prediction. Therefore, if you upload a large protein with more than one domain, more often than not you will only get accurate prediction for one of your domain. If you have a protein longer than 1,500 residues, you can split the sequence into domains either by Pfam search, or by ThreaDom. You can then submit the sequence of each domain separately. This should generate models of higher accuracy. You can then assemble individual domains into full length structure by DEMO.

5. How can I run I-TASSER suite on Mac, Windows or 32-bit Linux?

All components of I-TASSER suite were developed on 64-bit Linux. All its Fortran and C++ binary executables are compiled for 64-bit Linux only. This means that it is currently impossible to run I-TASSER suite on Mac OS. It is also impossible to run I-TASSER suite on any 32-bit system, including 32-bit Linux. As I-TASSER suite is memory intensive, there is no point trying to make I-TASSER run on 32-bit system where no more than 4Gb of memory could be addressed. It is impossible to run I-TASSER on Windows, including Windows Subsystem for Linux (also known as "Ubuntu on Windows").

6. Why my SAXSTER prediction did not return any result?

Usually, this happens when you submit invalid SAXS profile. For SAXSTER to work, you need to upload either SAXS Pair Distance Distribution Function p(r) or SAXS Intensity profile I(q). If your uploaded p(r) or I(q) profile is empty (all zeros) or contains at least one p(r) value smaller than zero or greater than one, SAXSTER will not work.

7. How can I use I-TASSER models to study the effect of mutations on the overall topology?

(Short answer) No, you cannot. Overall topology of I-TASSER models for different mutant of the same protein is usually very similar.

(Long answer) A structure model can tell you where is the mutation, e.g. if it is near ligand binding site, an active site, or at protein-protein interaction interface, etc. However, unless you have introduced a substantial number of mutations, or introduce long insertion/deletetion, different mutants of the same protein usually have similar final I-TASSSER structures. This is in accordance with our observation on experimental structure in PDB, wild type protein and mutant protein of a small number of substitution usually shares almost identical conformation, even if their function might differ significantly. We have developed a pipeline called STRUM to address the effect of single mutations on a protein, specifically the stability differences between native protein and its mutants.

8. How do I report bugs for web servers and bioinformatics tools in Yang Zhang lab?

If you have successfully submit jobs via web server, but the webserver did not send any result back after two weeks, you should check whether your input is incorrect. If you are sure it is a bug, please report it to yangzhanglab@umich.edu using the email you used for job submission and report the web service you used and your Job ID.

If you find a bug in standalone software downloaded from Yang Zhang lab website, such as I-TASSER suite, please report it to the Service System Discussion Board. You need to provide the following information: [1] input files, [2] output files, [3] command you used to run the software and its screen output, [4] if you recompile the software yourself, instead of using our precompiled binaries, please report the compiler version (e.g. gfortran 4.8) and compilation command you used, [5] the operating system (e.g. Ubuntu Linux Trusty 14.04 amd64, or Mac OSX 10.11.1 EL Capitan) and CPU description; under Linux please send the output of:

uname -a; lsb_release -a; head -n 25 /proc/cpuinfo; ulimit -a; free

9. What are the 'top 10 templates used by I-TASSER' in the Result page?

I-TASSER modeling starts from the structure templates identified by LOMETS from the PDB library. LOMETS is a meta-server threading approach containing multiple threading programs, where each program can generate tens of thousands of templates. I-TASSER only uses the templates of the highest significance in the threading alignments, which are measured by the Z-score (the difference between the raw and average scores in the unit of standard deviation). The top 10 templates are the 10 templates selected from the LOMETS threading programs. Usually, one (or two) template of the highest Z-score is selected from each threading program, where the threading programs are sorted by the average performance in the large-scale benchmark test experiments.

10. What is the 'top 5 models predicted by I-TASSER' in the Result page?

For each target, I-TASSER simulations generate tens of thousands conformations (called decoys). To select the final models, I-TASSER uses SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and report up to five models which corresponds to the five largest structure clusters. In Monte Carlo theory, the largest clusters correspond to the states of the largest partition function (or lowest free energy) and therefore have the highest confidence. The confidence of each model is quantitatively measured by C-score (see below). Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score. Although the first model has a higher C-score and a better quality in most cases, it is not unusual that the lower-rank models have a better quality than the higher-rank models. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.

11. What are 'Proteins structurally close to the target in the PDB' in the Result page?

After the structure-assembly simulation, I-TASSER use TM-align program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB which have the closest structural similarity (i.e. the highest TM-score) to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in 'Predicted function using COACH' to infer the biological function of the target protein, since COACH has been extensively trained to derive function from multi-source of sequence and structure features which has on average a much higher accuracy than the function annotations derived only from the global structure comparison.

12. What is C-score in the Result page?

C-score is a confidence score for estimating the quality of predicted models by I-TASSER. It is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5,2], where a C-score of higher value signifies a model with a high confidence and vice-versa.

13. What is TM-score in the Result page?

TM-score is a recently proposed scale for measuring the structural similarity between two structures (see Zhang and Skolnick, Scoring function for automated assessment of protein structure template quality, Proteins, 2004 57: 702-710). The purpose of proposing TM-score is to solve the problem of RMSD which is sensitive to the local error. Because RMSD is an average distance of all residue pairs in two structures, a local error (e.g. a misorientation of the tail) will arise a big RMSD value although the global topology is correct. In TM-score, however, the small distance is weighted stronger than the big distance which makes the score insensitive to the local modeling error. A TM-score >0.5 indicates a model of correct topology and a TM-score<0.17 means a random similarity. These cutoff does not depends on the protein length.

14. What is difference and relationship between C-score and TM-score?

TM-score (or RMSD) is a known standard for measuring structural similarity between two structures which are usually used to measure the accuracy of structure modeling when the native structure is known, while C-score is a metric that I-TASSER developed to estimate the confidence of the modeling. In case where the native structure is not known, it becomes necessary to predict the quality of the modeling prediction, i.e. what is the distance between the predicted model and the native structures? To answer this question, we tried predicted the TM-score and RMSD of the predicted models relative the native structures based on the C-score.

In a benchmark test set of 500 non-homologous proteins, we found that C-score is highly correlated with TM-score and RMSD. Correlation coefficient of C-score of the first model with TM-score to the native structure is 0.91, while the coefficient of C-score with RMSD to the native structure is 0.75. These data lay the base for the reliable prediction of the TM-score and RMSD using C-score. In the output section, I-TASSER only reports the quality prediction (TM-score and RMSD) for the first model, because it was found that the correlation between C-score and TM-score is weak for lower rank models. However, the C-score is listed for all models just for a reference.

15. Why some lower-rank models have higher C-score in the Result page?

We have found that the cluster size is more robust than C-score for ranking the predicted models. The final I-TASSER models are therefore ranked based on cluster size rather than C-score in the output. Nevertheless, the C-score has a strong correlation with the quality of the final models, which has been used to quantitatively estimate the RMSD and TM-score of the final models relative to the native structure. Unfortunately, such strong correlation only occurs for the first predicted model from the largest cluster. Thus, the C-scores of the lower-rank models (i.e., models 2-5) are listed only for reference and a comparison among them is not advised. In other word, even though the lower-rank models may have a higher C-score than the first model in some cases, the first model is on average the most reliable and should be considered if without special reasons (e.g., from biological sense or experimental data).

16. Why do I-TASSER models have worse ramachandran plot than other structure prediction program? How can I refine them using FG-MD and ModRefiner?

Different from traditional homology modelling programs that build structure models based on a single template, I-TASSER server builds models by reassembling the structural fragments from multiple templates. As a result, I-TASSER models sometime have more backbone torsion angles within energetically unfavorable regions in the Ramachandran plot; this happens more often for the difficult targets that have no close homologous templates. This does NOT mean I-TASSER is worse than homology modelling (in contrast, homologous models are almost certainly incorrect for these targets). When I-TASSER performs simulation, it generates thousands of decoy structures. These structures are clustered by structure similarity. The top structure model comes from structure averaging of largest cluster. The structure averaging improves the global topology (in terms of TM-score and RMSD between model and native structure). But it can make the local structure such as backbone torsion angles worse, for the hard targets in which the distribution of the structural decoys is diverged. At the end of the I-TASSER pipeline, FG-MD or ModRefiner is used to refine the structure to correct the local structures. So users do not have to further refine the structure themselves. In general, it is very difficult for structure refinement to further improve the local structure without worsening the global topology.

17. Why do I received only one model instead of top five models?

I-TASSER selects models by clustering the decoys that are generated in the Monte Carlo structural assembly simulations. When the decoy distribution is very converged, the clustering process may result in less than five clusters, or in extreme case only one cluster. This usually means that the model has a high confidence (or I-TASSER is so sure about the model that it does not need to predict more models).

18. What molecular graphic software should be used to visualize I-TASSER structure models?

I-TASSER predicted protein structures can be visualized by any molecular graphic software that supports the PDB format, including PyMOL, RasMol, Jmol, VMD, UCSF Chimera, and our in-house program MVP-Fit, among many others.
• JSmol/Jmol is used to dynamically render the structure applets on the I-TASSER output webpages. To reproduce the visual style of the I-TASSER output webpage in Jmol, you can follow this post.
• RasMol and PyMOL are the recommended programs to visualize structure superposition by TM-align or TM-score. RasMol and PyMOL scripts for superposed structures can be generated using the "-o" option in the TM-align/TM-score programs. Our servers use RasMol and PyMOL to generate static images.