I-TASSER results

Input Sequence in FASTA format

>protein (42 residues)
MMDPSPDYDVSDEIEFFFRYLTWGLRGVETGDGYPPPAYPPV

Predicted Secondary Structure

Sequence	20 40 \| \| MMDPSPDYDVSDEIEFFFRYLTWGLRGVETGDGYPPPAYPPV
Prediction	CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
Conf.Score	999999998875689999999877635789999999999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| MMDPSPDYDVSDEIEFFFRYLTWGLRGVETGDGYPPPAYPPV
Prediction	744464635354414233423321132245475244564468
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Normalized B-facotr

(B-factor is a value to indicate the extent of the inherent thermal mobility of residues/atoms in proteins. In I-TASSER, this value is deduced from threading template proteins from the PDB in combination with the sequence profiles derived from sequence databases. The reported B-factor profile in the figure below corresponds to the normalized B-factor of the target protein, defined by B=(B'-u)/s, where B' is the raw B-factor value, u and s are respectively the mean and standard deviation of the raw B-factors along the sequence. (Click here to read more about predicted normalized B-factor)

Top 10 threading templates used by I-TASSER

Rank

PDB
Hit

Iden1

Iden2

Cov

Norm.
Zscore

Download
Align.

                  20                  40

                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
MMDPSPDYDVSDEIEFFFRYLTWGLRGVETGDGYPPPAYPPV

1devB

0.21

0.19

0.90

1.19

MUSTER

SQSPNPN----NPAEYCSTIPPLQQAQASGALSSPPPTMVPV

2k2uB

0.25

0.19

0.76

1.26

dPPAS

PHDSAP-YGALDMADFEFEQMFTDALGIDEYGG---------

2k2uB

0.25

0.19

0.76

1.09

wdPPAS

PHDSAP-YGALDMADFEFEQMFTDALGIDEYGG---------

5lo9A2

0.23

0.21

0.95

0.92

wMUSTER

VSGQVPETN-GLVLDALQSYIFWLATGAPTGDAMSGRGYPR-

2fhoA

0.34

0.24

0.69

0.93

wPPAS

---GTPEWRWEREID---N------RPLSD-EGYPPAGYVPI

2k2uB

0.25

0.19

0.76

1.29

dPPAS2

PHDSAP-YGALDMADFEFEQMFTDALGIDEYGG---------

1devB

0.21

0.19

0.90

1.33

PPAS

SQSPNPN----NPAEYCSTIPPLQQAQASGALSSPPPTMVPV

3m6iA3

0.17

0.98

1.21

Env-PPAS

FGGIEPALECTG-VESSIAAAIWAVKGFVIGVGKNEIQIPFM

3kdrC2

0.17

0.98

1.14

MUSTER

LIEQTNNAQLSDDVDRIINGYVAARRGRNSGVGFSSSGLE-V

2k8fB

0.18

0.17

0.93

1.22

dPPAS

MEEPQSDPSVEPPLSQETFSDLWKL--LPENNVLSPLPSQA-

(a)	Iden1 is the number of template residues identical to query divided by number of aligned residues.
(b)	Iden2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment.
(e)	Download Align. list the threading program used to identify the template provide the 3D structure of aligned regions of threading templates.

Top 5 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that 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. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. 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.)

More about C-score

Local structure accuracy of first model

Download Model 1

C-score=-1.80

Estimated TM-score = 0.50±0.15

Estimated RMSD = 5.8±3.7Å

Download Model 2

C-score=-3.43

Download Model 3

C-score=-3.96

Download Model 4

C-score=-2.18

Download Model 5

C-score=-2.82

Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment 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 that 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 the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)

Top 10 Identified stuctural analogs in PDB

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov
1	2awyA	0.590	2.95	0.098	0.952
2	1h0nA	0.588	2.22	0.026	0.929
3	3l39A	0.587	3.05	0.024	1.000
4	3fmsA	0.584	2.87	0.073	0.952
5	3gi9C	0.582	2.58	0.024	0.976
6	2wj9A	0.580	2.57	0.098	0.976
7	3rauA2	0.577	2.21	0.071	0.905
8	4a01A	0.575	2.75	0.024	1.000
9	1wy1B	0.569	2.78	0.071	0.952
10	4eqyA	0.568	2.49	0.100	0.952

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)

Ligand binding sites

Rank	C-score	Cluster size	PDB Hit	Lig Name	Download Complex	Ligand Binding Site Residues
1	0.25	52	3sxkA	BCT	Rep, Mult	11,12,13
2	0.12	26	3ae2C	SLI	Rep, Mult	15,16,19
3	0.08	18	3rv5D	DXC	Rep, Mult	13,16,17,20
4	0.06	15	4kt0B	CLA	Rep, Mult	14,17,18,20,21,23,24
5	0.03	7	4il6H	CLA	Rep, Mult	21,25,28
6	0.02	4	1ximA	CO	Rep, Mult	7,9
7	0.02	5	2nr9A	PA6	Rep, Mult	21,25
8	0.02	6	3lbzA	Z89	Rep, Mult	19,22,23,26
9	0.01	2	2gjmA	UUU	Rep, Mult	3,5
10	0.00	1	2o011	CLA	Rep, Mult	28,29

	Download the all possible binding ligands and detailed prediction summary.
	Download the templates clustering results.
(a)	C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)	Cluster size is the total number of templates in a cluster.
(c)	Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)	Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column. Mult is the complex structures with all potential binding ligands in the cluster.

Enzyme Commission (EC) numbers and active sites

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov	EC Number	Active Site Residues
1	0.060	1ybhA	0.523	2.70	0.073	0.929	2.2.1.6	NA
2	0.060	1hplA	0.506	3.18	0.000	0.833	3.1.1.3	NA
3	0.060	1ethA	0.530	3.36	0.049	0.905	3.1.1.3	NA
4	0.060	2jf2A	0.538	2.82	0.100	0.952	2.3.1.129	NA
5	0.060	1ta9B	0.535	3.14	0.049	0.976	1.1.1.6	NA
6	0.060	2fp0B	0.536	3.02	0.000	0.905	3.2.1.143	NA
7	0.060	2gruA	0.536	3.04	0.000	1.000	4.2.3.-	NA
8	0.060	2e76A	0.537	3.08	0.048	0.881	1.10.99.1	21,25
9	0.060	1itwB	0.539	2.91	0.098	0.952	1.1.1.42	NA
10	0.060	1xagA	0.534	2.79	0.000	0.976	4.2.3.4	NA
11	0.060	1mhyD	0.533	2.98	0.024	0.976	1.14.13.25	NA
12	0.060	1jk0A	0.567	2.62	0.077	0.929	1.17.4.1	NA
13	0.060	1sqfA	0.552	2.90	0.025	0.905	2.1.1.-	NA
14	0.060	1nvbB	0.547	2.74	0.024	0.976	4.2.3.4	15,19
15	0.060	2j4lF	0.495	2.89	0.024	0.833	2.7.4.22	NA
16	0.060	2yr4A	0.538	2.87	0.128	0.929	1.13.12.9	NA
17	0.060	1ujnA	0.535	2.57	0.098	0.952	4.2.3.4	13
18	0.060	3erfA	0.542	3.18	0.077	0.905	2.5.1.18	NA
19	0.060	2b0tA	0.538	2.87	0.048	0.976	1.1.1.42	38

(a)	Cscore^EC is the confidence score for the EC number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Gene Ontology (GO) terms

Rank	Cscore^GO	TM-score	RMSD^a	IDEN^a	Cov	PDB Hit	Associated GO Terms
Homologous GO templates in PDB
0	0.07	0.566	2.31	0.05	0.93	4djnA	GO:0001822 GO:0003014 GO:0004748 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005971 GO:0006260 GO:0006264 GO:0006281 GO:0006974 GO:0006979 GO:0009186 GO:0009200 GO:0009263 GO:0014075 GO:0015949 GO:0016491 GO:0046872 GO:0055114 GO:0070062 GO:1902254
1	0.07	0.538	2.87	0.05	0.95	4bmqA	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016020 GO:0016021 GO:0016491 GO:0046872 GO:0055114
2	0.07	0.487	2.80	0.05	0.90	2hmqA	GO:0005344 GO:0005506 GO:0006810 GO:0015671 GO:0046872
3	0.07	0.518	2.80	0.07	0.95	2bq1I	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
4	0.07	0.540	2.64	0.10	0.88	4xpwA	GO:0005344 GO:0006810 GO:0015671 GO:0046872
5	0.07	0.543	2.77	0.07	0.93	1a7dA	GO:0005344 GO:0005506 GO:0006810 GO:0015671 GO:0046872
6	0.07	0.500	2.66	0.05	0.88	3j7y5	GO:0003735 GO:0005739 GO:0005743 GO:0005761 GO:0005840 GO:0006412 GO:0030529 GO:0044822 GO:0070125 GO:0070126
7	0.07	0.571	2.75	0.07	0.93	3waqA	GO:0004871 GO:0007165 GO:0016020 GO:0016021 GO:0046872
8	0.07	0.493	3.14	0.05	0.79	4p9fA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
9	0.07	0.503	3.45	0.07	0.88	3dxpA	GO:0016740
10	0.07	0.520	2.98	0.00	0.93	1h9tA	GO:0000062 GO:0003677 GO:0003700 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0006629 GO:0006631 GO:0019217 GO:0019395 GO:0045723 GO:0045892 GO:0045893
11	0.07	0.523	2.70	0.08	0.93	4m1hB	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
12	0.07	0.559	2.85	0.15	0.93	1hrbA	GO:0005344 GO:0005506 GO:0006810 GO:0015671 GO:0046872
13	0.07	0.552	2.88	0.05	0.95	4n83A	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
14	0.07	0.549	2.66	0.03	0.93	2o1zA	GO:0009186 GO:0016491 GO:0046872 GO:0055114
15	0.07	0.500	3.20	0.07	0.95	3qcpA	GO:0000166 GO:0003756 GO:0005615 GO:0006457 GO:0016020 GO:0016021 GO:0016491 GO:0016971 GO:0016972 GO:0030173 GO:0045454 GO:0055114
16	0.07	0.508	2.75	0.05	0.95	4m1fA	GO:0004748 GO:0005506 GO:0005737 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0030145 GO:0046872 GO:0055114
17	0.07	0.559	2.34	0.03	0.93	2vuxB	GO:0001822 GO:0003014 GO:0004748 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005971 GO:0006260 GO:0006264 GO:0006281 GO:0006974 GO:0006979 GO:0009186 GO:0009200 GO:0009263 GO:0014075 GO:0015949 GO:0016491 GO:0046872 GO:0055114 GO:0070062 GO:1902254
18	0.07	0.588	2.22	0.03	0.93	1h0nA	GO:0004748 GO:0005634 GO:0005737 GO:0005971 GO:0006260 GO:0009186 GO:0009262 GO:0009263 GO:0016491 GO:0046872 GO:0051259 GO:0051290 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0043169	GO:0061731
GO-Score	0.58	0.37
Biological Processes	GO:0034645	GO:0006259	GO:0009132	GO:0009165	GO:1901137	GO:0009262
GO-Score	0.37	0.37	0.37	0.37	0.37	0.37
Cellular Component	GO:0044445	GO:1990204
GO-Score	0.37	0.37

(a)	Cscore^GO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.
(f)	The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on Cscore^GO of the template.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Please cite the following articles when you use the I-TASSER server:
1.	J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2.	J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.	A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.	Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.

I-TASSER results for job id Rv0157A

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]