D-I-TASSER example

D-I-TASSER results for example

[Click result.zip to download all results on this page]

Input Sequence in FASTA format

>test (69 residues)
AGCNAGQLTVCTGAIAGGARPTAACCSSLRAQQGCFCQFAKDPRYGRYVNSPNARKAVSS
CGIALPTCH

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| AGCNAGQLTVCTGAIAGGARPTAACCSSLRAQQGCFCQFAKDPRYGRYVNSPNARKAVSSCGIALPTCH
Prediction	CCCCHHHCCCCHHHHHCCCCCCHHHHHHHHHCCCCHHHHHCCCCHHHHCCCHHHHHHHHHHCCCCCCCC
Confidence	977733312136776379999599999999615501111119537753688889999997199999889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| AGCNAGQLTVCTGAIAGGARPTAACCSSLRAQQGCFCQFAKDPRYGRYVNSPNARKAVSSCGIALPTCH
Prediction	761545414423433346652355015404744412041253441451253640431052163334628
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (right figure) derived based on confidence scores of AttentionPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60

                   |                   |                   |

SS
Seq

CCCCHHHCCCCHHHHHCCCCCCHHHHHHHHHCCCCHHHHHCCCCHHHHCCCHHHHHHHHHHCCCCCCCC
AGCNAGQLTVCTGAIAGGARPTAACCSSLRAQQGCFCQFAKDPRYGRYVNSPNARKAVSSCGIALPTCH

1tukA

0.56

0.54

15.43

1.33

DEthreader

ACQASQ-LAVCASAILSGAKPSGECCGNLRAQQGCFCQYAKDPTYGQ-YRSPHARDTLTSCGLAVPHC-

1tukA

0.60

0.58

16.62

3.23

HHpred

-ACQASQLAVCASAILSGAKPSGECCGNLRAQQGCFCQYAKDPTYGQYIRSPHARDTLTSCGLAVPHC-

1siyA

0.21

0.20

6.43

1.48

DisCoVER

MTCVQGNLAQCIGFLQKGGVVPPSCCTGVKNILAVCSCLKAA--AVRGINPNNAEALPGKCGVYKIST-

1tukA

0.60

0.58

16.62

3.00

SPARKS-K

-ACQASQLAVCASAILSGAKPSGECCGNLRAQQGCFCQYAKDPTYGQYIRSPHARDTLTSCGLAVPHC-

1tukA

0.61

0.58

16.61

1.32

MapAlign

--CQASQLAVCASAILSGAKPSGECCGNLRAQQGCFCQYAKDPTYGQYIRSPHARDTLTSCGLAVPHC-

1tukA

0.60

0.58

16.62

1.11

FFAS-3D

-ACQASQLAVCASAILSGAKPSGECCGNLRAQQGCFCQYAKDPTYGQYIRSPHARDTLTSCGLAVPHC-

1tukA

0.59

0.57

16.22

1.17

Hybrid-CEthreader

-ACQASQLAVCASAILSGAKPSGECCGNLRAQQGCFCQYAKDPTYGQ-YRSPHARDTLTSCGLAVPHC-

2ljoA

0.23

0.22

6.83

1.17

DEthreader

ICAVTSDLSPCLTYLTGGPGPSPQCCGGVKKLLAA-CNL-KS-AAGSILNTNNAAALPGKCGVNIYKTN

1l6hA

1.00

28.00

3.02

HHpred

AGCNAGQLTVCTGAIAGGARPTAACCSSLRAQQGCFCQFAKDPRYGRYVNSPNARKAVSSCGIALPTCH

2rknA

0.25

7.65

2.08

SPARKS-K

DLCSQDELNECKPAVSKETSPSQPCCTALQHDFACLCGYKNSPWLGFGVDPELASALPKQCGLANAPTC

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 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 and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download PDB	Download ModelCIF	C-score^b	Estimated TM-score^c	Estimated RMSD^c
	1	model1.pdb.gz	model1.cif	-0.19	0.77±0.12	3.6±2.5Å

(a)	D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.
(b)	The model confidence is quantitatified by C-score, calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of AttentionPotential, and convergence of D-I-TASSER simulations. C-score is typically in the range of [-5, 2], with higher C-score signifies higher model confidence.
(c)	Model TM-score and RMSD are estimated based on C-score and protein length for the first model.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	1tukA	0.90	1.10	0.582	0.971	model1_1tukA.pdb.gz
2	2ljoA	0.71	2.21	0.227	0.957	model1_2ljoA.pdb.gz
3	7ksbA	0.70	2.36	0.269	0.971	model1_7ksbA.pdb.gz
4	5tviV	0.69	2.34	0.288	0.957	model1_5tviV.pdb.gz
5	4xuwA	0.69	2.29	0.258	0.957	model1_4xuwA.pdb.gz
6	6frrA	0.69	2.22	0.200	0.942	model1_6frrA.pdb.gz
7	2rknA	0.68	2.37	0.242	0.957	model1_2rknA.pdb.gz
8	1siyA	0.67	2.59	0.224	0.971	model1_1siyA.pdb.gz
9	7kscA	0.65	2.77	0.203	1.000	model1_7kscA.pdb.gz
10	1bv2A	0.64	2.64	0.279	0.986	model1_1bv2A.pdb.gz

(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 Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0008289	0.89	lipid binding
GO:0043167	0.77	ion binding
GO:0046872	0.75	metal ion binding
GO:0043168	0.74	anion binding
GO:0043621	0.72	protein self-association
GO:0008270	0.72	zinc ion binding
GO:0005504	0.72	fatty acid binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0009862	0.72	systemic acquired resistance, salicylic acid mediated signaling pathway
GO:0071702	0.60	organic substance transport

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044464	1.00	cell part
GO:0043229	0.75	intracellular organelle
GO:0043231	0.63	intracellular membrane-bounded organelle
GO:0031225	0.60	anchored component of membrane

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	1ac5A	0.509	3.66	0.047	0.913	3.4.16.6	NA
2	0.060	3kaoA	0.507	3.54	0.094	0.841	4.1.2.40	NA
3	0.060	1bx9A	0.508	3.39	0.031	0.927	2.5.1.18	NA
4	0.060	3a1kA	0.493	2.91	0.066	0.855	3.5.1.4	NA
5	0.060	1clcA	0.508	3.43	0.016	0.884	3.2.1.4	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (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.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.03	1jtbA	0.591	3.15	0.217	0.986	0.50	UUU	complex1.pdb.gz	4,5,8,29,43,54,57,58,63,65

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	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.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Qiqige Wuyun, Peter L Freddolino, Yang Zhang. Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15. Proteins. 2023; 1-20. doi:10.1002/prot.26585.