D-I-TASSER DIT3499

D-I-TASSER results for DIT3499

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

Input Sequence in FASTA format

>Dicer (30 residues)
HAEGTFTSDVSSYLEGQAAKEFIAWLVRGR

Predicted Secondary Structure

Sequence	20 \| HAEGTFTSDVSSYLEGQAAKEFIAWLVRGR
Prediction	CCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
Confidence	998750113799999999999999998089
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 \| HAEGTFTSDVSSYLEGQAAKEFIAWLVRGR
Prediction	867343464035215753255015214748
	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

                   |

SS
Seq

CCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
HAEGTFTSDVSSYLEGQAAKEFIAWLVRGR

5y6qC2

0.03

1.90

1.00

DEthreader

SQLAGNLTAAVNDTAKKMRERLLALASEPS

6w1sW

0.07

2.80

1.67

DEthreader

DQVIKEDVSELRSELQRKDALVQKHLTKLR

5azsA

0.13

4.60

1.50

DEthreader

VAEVSQAYLSYDGALRRLALTRQTLVSREY

2obuA

0.37

10.90

1.56

SPARKS-K

YAEGTFISDYSIAMDKIHQQDFVNWLLAQK

1ulvA

0.07

2.80

1.08

MapAlign

SQIAALAAAADIAGKAGSAAVYRATADEWQ

1q35A

0.10

3.70

0.52

CEthreader

SYNVSLFAAMIEHYGIEKTKAFLEGLKANL

2obuA

0.37

10.90

1.09

MUSTER

YAEGTFISDYSIAMDKIHQQDFVNWLLAQK

2obuA

0.37

10.90

1.18

HHsearch

YAEGTFISDYSIAMDKIHQQDFVNWLLAQK

2obuA

0.37

10.90

0.75

FFAS-3D

YAEGTFISDYSIAMDKIHQQDFVNWLLAQK

1jrjA

0.53

15.40

0.42

CNFpred

HGEGTFTSDLSKQMEEEAVRLFIEWLKNGG

(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 3 final models from D-I-TASSER

Click to view	Rank^a	Download PDB	Download ModelCIF	Estimated TM-score^b
	1	model1.pdb.gz	model1.cif	0.35
	2	model2.pdb.gz		0.19
	3	model3.pdb.gz		0.19

(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 estimated TM-score (eTM-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. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

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	7rkcA2	0.85	1.55	0.067	1.000	model1_7rkcA2.pdb.gz
2	7c2xA	0.84	0.79	0.000	1.000	model1_7c2xA.pdb.gz
3	7wvtA	0.84	0.84	0.000	0.967	model1_7wvtA.pdb.gz
4	7k5cH1	0.84	0.98	0.067	1.000	model1_7k5cH1.pdb.gz
5	6bfiA	0.84	1.11	0.033	1.000	model1_6bfiA.pdb.gz
6	6rw9A	0.83	1.64	0.100	1.000	model1_6rw9A.pdb.gz
7	7eqdH	0.83	0.75	0.067	1.000	model1_7eqdH.pdb.gz
8	5a5tH	0.83	1.26	0.067	1.000	model1_5a5tH.pdb.gz
9	3bj4B	0.83	1.30	0.067	0.967	model1_3bj4B.pdb.gz
10	4xwhA	0.83	1.14	0.000	0.967	model1_4xwhA.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:0005102	1.00	receptor binding
GO:0031769	0.95	glucagon receptor binding
GO:0005179	0.85	hormone activity

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:0065007	0.96	biological regulation
GO:0050789	0.95	regulation of biological process
GO:0065008	0.93	regulation of biological quality
GO:0048519	0.93	negative regulation of biological process
GO:0048583	0.92	regulation of response to stimulus
GO:0048585	0.65	negative regulation of response to stimulus
GO:0032099	0.63	negative regulation of appetite
GO:0050794	0.53	regulation of cellular process

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:0005615	1.00	extracellular space
GO:0044464	0.71	cell part

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	0.079	1qleD	0.690	1.68	0.067	0.967	1.9.3.1	NA
2	0.076	3brtA	0.668	1.42	0.069	0.933	2.7.11.10	NA
3	0.070	3e7kH	0.774	1.56	0.033	0.967	2.7.11.1	NA
4	0.067	1wt6B	0.821	0.61	0.071	0.933	2.7.11.1	NA
5	0.067	3brvC	0.739	1.63	0.033	1.000	2.7.11.10	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.05	2ojeD	0.825	0.86	0.100	1.000	0.49	III	complex1.pdb.gz	21,22,25,26
2	0.03	2r6tA	0.820	0.69	0.067	0.933	0.44	ATP	complex2.pdb.gz	1,2,3,7,11,14
3	0.03	3f33A	0.780	1.46	0.033	0.967	0.81	PFL	complex3.pdb.gz	14,17,18,21
4	0.02	2g380	0.790	1.59	0.067	0.967	0.47	III	complex4.pdb.gz	2,6,9,10,13,14,17,20,23,24,27,28
5	0.02	3f34A	0.782	1.45	0.033	0.967	0.41	DIE	complex5.pdb.gz	22,25,26

	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.
2.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.