DeepFold results for Example

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

Input Sequence in FASTA format

>tsam (347 residues)
MFIRNCWYVAAWDTEIPAEGLFHRTLLNEPVLLYRDTQGRVVALENRCCHRSAPLHIGRQ
EGDCVRCLYHGLKFNPSGACVEIPGQEQIPPKTCIKSYPVVERNRLVWIWMGDPARANPD
DIVDYFWHDSPEWRMKPGYIHYQANYKLIVDNLLDFTHLAWVHPTTLGTDSAASLKPVIE
RDTTGTGKLTITRWYLNDDMSNLHKGVAKFEGKADRWQIYQWSPPALLRMDTGSAPTGTG
APEGRRVPEAVQFRHTSIQTPETETTSHYWFCQARNFDLDDEALTEKIYQGVVVAFEEDR
TMIEAHEKILSQVPDRPMVPIAADAGLNQGRWLLDRLLKAENGGTAP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| MFIRNCWYVAAWDTEIPAEGLFHRTLLNEPVLLYRDTQGRVVALENRCCHRSAPLHIGRQEGDCVRCLYHGLKFNPSGACVEIPGQEQIPPKTCIKSYPVVERNRLVWIWMGDPARANPDDIVDYFWHDSPEWRMKPGYIHYQANYKLIVDNLLDFTHLAWVHPTTLGTDSAASLKPVIERDTTGTGKLTITRWYLNDDMSNLHKGVAKFEGKADRWQIYQWSPPALLRMDTGSAPTGTGAPEGRRVPEAVQFRHTSIQTPETETTSHYWFCQARNFDLDDEALTEKIYQGVVVAFEEDRTMIEAHEKILSQVPDRPMVPIAADAGLNQGRWLLDRLLKAENGGTAP
Prediction	CCCCCCSSSSSSHHHCCCCCCSSSSSCCSSSSSSSCCCCCSSSSSCCCCCCCCCCCCCSSSCCSSSCCCCCCSSCCCCCSSSCCCCCCCCCCCCCCCCSSSSSCCSSSSSCCCCCCCCCCHHCCHHCCCCCCCSSSCSSSSSCCCHHHHHHHHHCCCCHHCCCCCHCCCCCHHHCCCSSSSSCCCCCSSSSSSSSSCCCCCHHHHHCCCCCCCCCSSSSSSSCCCSSSSSSCCCCCCCCCCCCCCCCCCCCSSSSSSSSCCCCCCSSSSSSSSSCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCC
Confidence	97678269999899999998479999888899998899998999896688899620086649979879988587999987658998899966479811389998979993299224992056022402697623325699997982267889865242160394010898235348879995179915899999828864234321001369701458999808948998655689888899987788860899999992478998999999863889991899999989879999999999999999982399999999737399999999999999993479999
	H:Helix; S:Strand; C:Coil

Predicted Spatial Restraints Used in the DeepFold Simulations

Contact Map

Distance Map

Orientation Map

The DeepFold simulations are guided by the consensus contact map (left figure), distance map (middle figure) and orientations (right figure). In the contact and distance maps, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair predicted to form a contact, while for the distance and orientation maps, a color scale represents a distance of 1-20+ angstroms or 0-360 degrees, respectively.

Top model from DeepFold

Click to view	Rank^a	Download
	1	model1.pdb.gz

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	3gobA	0.88	2.20	0.340	0.957	CON_model_3gobA.pdb.gz
2	4qdcA	0.80	2.97	0.145	0.916	CON_model_4qdcA.pdb.gz
3	6wn3A	0.80	2.70	0.218	0.890	CON_model_6wn3A.pdb.gz
4	6iclA	0.79	2.65	0.228	0.885	CON_model_6iclA.pdb.gz
5	6ickA	0.78	2.51	0.242	0.870	CON_model_6ickA.pdb.gz
6	2zylA	0.78	3.12	0.142	0.908	CON_model_2zylA.pdb.gz
7	4qdfB	0.77	3.01	0.129	0.893	CON_model_4qdfB.pdb.gz
8	3gcfO	0.76	3.57	0.193	0.908	CON_model_3gcfO.pdb.gz
9	3gkqA	0.76	3.42	0.193	0.893	CON_model_3gkqA.pdb.gz
10	1z01A	0.76	3.32	0.174	0.893	CON_model_1z01A.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:0051536	0.96	iron-sulfur cluster binding
GO:0051537	0.95	2 iron, 2 sulfur cluster binding
GO:0005506	0.94	iron ion binding
GO:0003824	0.83	catalytic activity
GO:0016491	0.75	oxidoreductase activity
GO:0016705	0.60	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0051213	0.53	dioxygenase 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:0044237	0.99	cellular metabolic process
GO:0044710	0.98	single-organism metabolic process
GO:0044248	0.96	cellular catabolic process
GO:0006725	0.96	cellular aromatic compound metabolic process
GO:0055114	0.94	oxidation-reduction process
GO:0019439	0.94	aromatic compound catabolic process
GO:0071704	0.81	organic substance metabolic process
GO:1901360	0.54	organic cyclic compound metabolic 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:0044464	1.00	cell part
GO:0044424	0.92	intracellular part
GO:0044446	0.77	intracellular organelle part
GO:0044444	0.77	cytoplasmic part
GO:0043231	0.77	intracellular membrane-bounded organelle
GO:0044434	0.68	chloroplast part
GO:0009507	0.68	chloroplast
GO:0009941	0.53	chloroplast envelope
GO:0016020	0.50	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	0.507	1wqlA	0.748	3.83	0.114	0.928	1.14.12.-	70
2	0.443	1z01A	0.757	3.32	0.174	0.893	1.14.13.61	155,158,70
3	0.408	3en1A	0.749	3.72	0.134	0.919	1.14.12.11	155,158,70
4	0.145	1uliC	0.743	3.82	0.137	0.916	1.14.12.18	70
5	0.093	2b1xA	0.747	3.63	0.146	0.905	1.14.12.12	70

	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	0.72	3gkeA	0.882	2.16	0.338	0.963	1.62	FES	complex1.pdb.gz	48,50,51,53,67,69,70,71,72

	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.	Robin Pearce, Yang Li, Gilbert S. Omenn, Yang Zhang. Fast and Accurate Ab Initio Protein Structure Prediction Using Deep Learning Spatial Restraints. Submitted, 2021.