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DMFold results for example

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Input Sequence In FASTA Format

example ( 1221 residues )

>example-A
EIMPLTLKVNGKTEQLEVDTRTTLLDTLRENLHLIGTKKGCDHGQCGACTVLVNGRRLNACLTLAVMHQGAEITTIEGLGSPDNLHPMQAAFIKHDGFQCGYCTSGQICSSVAVLKEIQDGIPSHVTVDLVSAPETTADEIRERMSGNICRCGAYANILAAIEDAAGEIKS

>example-B
MKAFTYERVNTPAEAALSAQRVPGAKFIAGGTNLLDLMKLEIETPTHLIDVNGLGLDKIEVTDAGGLRIGALVRNTDLAAHERVRRDYAVLSRALLAGASGQLRNQATTAGNLLQRTRCPYFYDTNQPCNKRLPGSGCAALEGFSRQHAVVGVSEACIATHPSDMAVAMRLLDAVVETITPEGKTRSITLADFYHPPGKTPHIETALLPGELIVAVTLPPPLGGKHIYRKVRDRASYAFALVSVAAIIQPDGSGRVALGGVAHKPWRIEAADAQLSQGAQAVYDTLFASAHPTAENTFKLLLAKRTLASVLAEARAQA

>example-C
MKFDKPAGENPIDQLKVVGRPHDRIDGPLKTTGTARYAYEWHEEAPNAAYGYIVGSAIAKGRLTALDTDAAQKAPGVLAVITASNAGALGKGDKNTARLLGGPTIEHYHQAIALVVAETFEQARAAASLVQAHYRRNKGAYSLADEKQAVNQPPEDTPDKNVGDFDGAFTSAAVKIDATYTTPDQSHMAMEPHASMAVWDGNKLTLWTSNQMIDWCRTDLAKTLKVPVENVRIISPYIGGGFGGKLFLRSDALLAALAARAVKRPVKVMLPRPSIPNNTTHRPATLQHLRIGADQSGKITAISHESWSGNLPGGTPETAVQQSELLYAGANRHTGLRLATLDLPEGNAMRAPGEAPGLMALEIAIDELAEKAGIDPVEFRILNDTQVDPADPTRCFSRRQLIECLRTGADKFGWKQRNATPGQVRDGEWLVGHGVAAGFRNNLLEKSGARVHLEQNGTVTVETDMTDIGTGSYTILAQTAAEMLGVPLEQVAVHLGDSSFPVSAGSGGQWGANTSTSGVYAACMKLREMIASAVGFDPEQSQFADGKITNGTRSATLHEATAGGRLTAEESIEFGTLSKEYQQSTFAGHFVEVGVHSATGEVRVRRMLAVCAAGRILNPKTARSQVIGAMTMGMGAALMEELAVDDRLGYFVNHDMAGYEVPVHADIPKQEVIFLDDTDPISSPMKAKGVGELGLCGVSAAIANAVYNATGIRVRDYPITLDKLLDKLPDVV

Multiple Sequence Alignments

Alignment depth: Nf=123.769, number of sequences=4849

Download multiple sequence alignment in aln format.

Download multiple sequence alignment in a3m format.

Predicted Contact And Distance Map

Contact Map

Distance Map

Individual Chain Modeling Results

ID. of chain	chain	Length of chain	pLDDT	Models of Chain	Sequence
A	example-model1-A	171	0.97		EIMPLTLKVNGKTEQLEVDTRTTLLDTLRENLHLIGTKKGCDHGQCGACTVLVNGRRLNACLTLAVMHQGAEITTIEGLGSPDNLHPMQAAFIKHDGFQCGYCTSGQICSSVAVLKEIQDGIPSHVTVDLVSAPETTADEIRERMSGNICRCGAYANILAAIEDAAGEIKS
B	example-model1-B	318	0.97		MKAFTYERVNTPAEAALSAQRVPGAKFIAGGTNLLDLMKLEIETPTHLIDVNGLGLDKIEVTDAGGLRIGALVRNTDLAAHERVRRDYAVLSRALLAGASGQLRNQATTAGNLLQRTRCPYFYDTNQPCNKRLPGSGCAALEGFSRQHAVVGVSEACIATHPSDMAVAMRLLDAVVETITPEGKTRSITLADFYHPPGKTPHIETALLPGELIVAVTLPPPLGGKHIYRKVRDRASYAFALVSVAAIIQPDGSGRVALGGVAHKPWRIEAADAQLSQGAQAVYDTLFASAHPTAENTFKLLLAKRTLASVLAEARAQA
C	example-model1-C	732	0.99		MKFDKPAGENPIDQLKVVGRPHDRIDGPLKTTGTARYAYEWHEEAPNAAYGYIVGSAIAKGRLTALDTDAAQKAPGVLAVITASNAGALGKGDKNTARLLGGPTIEHYHQAIALVVAETFEQARAAASLVQAHYRRNKGAYSLADEKQAVNQPPEDTPDKNVGDFDGAFTSAAVKIDATYTTPDQSHMAMEPHASMAVWDGNKLTLWTSNQMIDWCRTDLAKTLKVPVENVRIISPYIGGGFGGKLFLRSDALLAALAARAVKRPVKVMLPRPSIPNNTTHRPATLQHLRIGADQSGKITAISHESWSGNLPGGTPETAVQQSELLYAGANRHTGLRLATLDLPEGNAMRAPGEAPGLMALEIAIDELAEKAGIDPVEFRILNDTQVDPADPTRCFSRRQLIECLRTGADKFGWKQRNATPGQVRDGEWLVGHGVAAGFRNNLLEKSGARVHLEQNGTVTVETDMTDIGTGSYTILAQTAAEMLGVPLEQVAVHLGDSSFPVSAGSGGQWGANTSTSGVYAACMKLREMIASAVGFDPEQSQFADGKITNGTRSATLHEATAGGRLTAEESIEFGTLSKEYQQSTFAGHFVEVGVHSATGEVRVRRMLAVCAAGRILNPKTARSQVIGAMTMGMGAALMEELAVDDRLGYFVNHDMAGYEVPVHADIPKQEVIFLDDTDPISSPMKAKGVGELGLCGVSAAIANAVYNATGIRVRDYPITLDKLLDKLPDVV
Click the Chain column or image, you can go into the individual page to check the individual Chain modeling results.

Top 5 Final Models From DMFold

Rank	Download PDB	pTM-score
1	model1.pdb.gz	0.97
2	model2.pdb.gz	0.97
3	model3.pdb.gz	0.97
4	model4.pdb.gz	0.97
5	model5.pdb.gz	0.97

Note: If the JSmol model is not visible, please refresh the page or click the radio buttons

(a)	DMFold generates a large set of structural models by different MSAs as inputs. These models are ranked by predicted TM-score (pTM-score for multimer) or predicted LDDT (pLDDT for monomer) and top 5 models are selected with the highest predicted scores.

Residue-level Modeling Quality

pLDDT of chain A

pLDDT of chain B

pLDDT of chain C

Proteins With Similar Structure

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

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	5g5g	0.99	0.33	1.00	0.99	Download
2	5y6q	0.94	2.25	0.42	0.97	Download
3	1rm6	0.91	2.72	0.28	0.95	Download
4	1sb3	0.91	2.76	0.29	0.95	Download
5	1t3q	0.90	2.58	0.26	0.93	Download
6	1n62	0.89	2.78	0.25	0.93	Download
7	1n60	0.89	2.78	0.25	0.93	Download
8	1n61	0.89	2.83	0.25	0.93	Download
9	1n63	0.89	2.83	0.25	0.93	Download
10	1zxi	0.89	2.85	0.25	0.93	Download

Note: If the JSmol model is not visible, please refresh the page or click the radio buttons

(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 US-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	Freq^GO	Chain ID	Name
GO:0016491	1.00	A,B,C	oxidoreductase activity
GO:1901363	1.00	A,B,C	heterocyclic compound binding
GO:0097159	1.00	A,B,C	organic cyclic compound binding
GO:0016903	1.00	A,B,C	oxidoreductase activity, acting on the aldehyde or oxo group of donors
GO:0050660	1.00	A,B,C	flavin adenine dinucleotide binding
GO:0016726	0.67	A,C	oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
GO:0004854	0.67	A,C	xanthine dehydrogenase activity
GO:0000166	0.33	B	nucleotide binding
GO:0050662	0.33	C	coenzyme binding

Download full result of the above freq.

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)

Freq^GO is the frequency of predicted GO terms with a Cscore^GO greater than 0.5 among all terms within each chain of a complex protein. The Freq^GO values range between [0-1], where a higher value indicates a greater proportion of high-confidence predictions (Cscore^GO > 0.5) in the function annotation of the protein chain.

(c)

Chain ID indicates the specific protein chain in the complex that contains the GO term with a Cscore^GO greater than 0.5. This identifier helps in associating high-confidence GO terms with their respective chains.

(d)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function.

[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 Freq^GO Chain ID Name

GO:0044710 1.00 A,B,C single-organism metabolic process

GO:0044237 1.00 A,B,C cellular metabolic process

GO:0044763 1.00 A,B,C single-organism cellular process

GO:1901564 1.00 A,B,C organonitrogen compound metabolic process

GO:0044281 1.00 A,B,C small molecule metabolic process

GO:0006139 1.00 A,B,C nucleobase-containing compound metabolic process

GO:0072521 1.00 A,B,C purine-containing compound metabolic process

GO:1901565 1.00 A,B,C organonitrogen compound catabolic process

GO:1901361 1.00 A,B,C organic cyclic compound catabolic process

GO:0044712 1.00 A,B,C single-organism catabolic process

GO:0009115 1.00 A,B,C xanthine catabolic process

GO:0055086 0.67 A,B nucleobase-containing small molecule metabolic process

GO:0046700 0.67 A,B heterocycle catabolic process

GO:0044270 0.67 A,B cellular nitrogen compound catabolic process

GO:0019439 0.67 A,C aromatic compound catabolic process

GO:0009112 0.67 A,C nucleobase metabolic process

GO:0006145 0.67 A,B purine nucleobase catabolic process

GO:0055114 0.67 A,B oxidation-reduction process

GO:0009987 0.33 B cellular process

GO:0008152 0.33 B metabolic process

GO:0044699 0.33 B single-organism process

GO:0071704 0.33 B organic substance metabolic process

GO:1901360 0.33 B organic cyclic compound metabolic process

GO:0046483 0.33 B heterocycle metabolic process

GO:0044238 0.33 B primary metabolic process

GO:0006807 0.33 B nitrogen compound metabolic process

GO:0044248 0.33 B cellular catabolic process

GO:0006144 0.33 B purine nucleobase metabolic process

GO:0072523 0.33 B purine-containing compound catabolic process

Download full result of the above freq.

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) Freq^GO is the frequency of predicted GO terms with a Cscore^GO greater than 0.5 among all terms within each chain of a complex protein. The Freq^GO values range between [0-1], where a higher value indicates a greater proportion of high-confidence predictions (Cscore^GO > 0.5) in the function annotation of the protein chain.

(c) Chain ID indicates the specific protein chain in the complex that contains the GO term with a Cscore^GO greater than 0.5. This identifier helps in associating high-confidence GO terms with their respective chains.

(d) The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process.

[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 Freq^GO Chain ID Name

GO:0044464 0.67 A,B cell part

GO:0044424 0.67 A,C intracellular part

GO:0005829 0.67 A,C cytosol

GO:0042597 0.33 B periplasmic space

GO:0016020 0.33 B membrane

Download full result of the above freq.

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) Freq^GO is the frequency of predicted GO terms with a Cscore^GO greater than 0.5 among all terms within each chain of a complex protein. The Freq^GO values range between [0-1], where a higher value indicates a greater proportion of high-confidence predictions (Cscore^GO > 0.5) in the function annotation of the protein chain.

(c) Chain ID indicates the specific protein chain in the complex that contains the GO term with a Cscore^GO greater than 0.5. This identifier helps in associating high-confidence GO terms with their respective chains.

(d) The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component.

[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 EC Number

Rank	Freq^EC	Chain ID	EC Number	EC Name
1	1.00	A,B,C	1.2.99.2	Carbon-monoxide dehydrogenase (acceptor)
2	1.00	A,B,C	1.17.3.2	Xanthine oxidase
3	1.00	A,B,C	1.17.1.4	Xanthine dehydrogenase
4	0.67	B,C	1.1.1.204	Transferred entry: 1.17.1.4
5	0.33	A	1.3.99.1	Succinate dehydrogenase

(a)	Freq^EC is the frequency of predicted Enzyme Commission (EC) number among all terms within each chain of a complex protein, considering only those terms with a TM-score greater than 0.4 for PDB-hits. Freq^EC values range in between [0-1];
(b)	Chain ID indicates the specific protein chain in the complex that contains the Enzyme Commission (EC) number.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Complex	Lig. Name
1	5g5g	0.993	0.33	1.000	0.994	Download	ACT C L CSD FAD FES GOL IOD MCN MOS SF4
2	5y6q	0.937	2.25	0.420	0.967	Download	FAD FES GOL IPA MCN MOS SF4 SO4
3	1rm6	0.908	2.72	0.280	0.952	Download	C L EPE FAD FES N A PCD SF4
4	1sb3	0.907	2.76	0.290	0.952	Download	EPE FAD FES PCD SF4
5	1t3q	0.896	2.58	0.260	0.934	Download	FAD FES GOL MCN SMO SO4
6	1n62	0.888	2.78	0.250	0.931	Download	CUB FAD FES MCN PO4
7	1n60	0.888	2.78	0.250	0.931	Download	FAD FES MCN OMO PO4
8	1n61	0.887	2.83	0.250	0.931	Download	CUN FAD FES MCN PO4
9	1n63	0.886	2.83	0.250	0.931	Download	CUN FAD FES MCN PO4
10	1zxi	0.886	2.85	0.250	0.931	Download	C U CUM FAD FES MCN PO4

Note: If the JSmol model is not visible, please refresh the page or click the radio buttons

	Click on the PDB hit radio buttons to visualize all predicted binding ligands.
	Click on the Lig Name radio buttons to visualize selected binding ligand and residues.
(a)	TM-score is a measure of global structural similarity between query and template protein.
(b)	RMSD^a the RMSD between residues that are structurally aligned by US-align.
(c)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(d)	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.

Download full result of the above ligand binding prediction.

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Reference:

Wei Zheng, Qiqige Wuyun, Yang Li, Chengxin Zhang, P Lydia Freddolino, Yang Zhang. Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nature Methods, (2024). https://doi.org/10.1038/s41592-023-02130-4.

Wei Zheng, Quancheng Liu, Qiqige Wuyun, P. Lydia Freddolino, Yang Zhang. DMFold: A deep learning platform for protein complex structure and function predictions based on DeepMSA2. In preparation.

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. 1-20. Proteins. (2023). doi:10.1002/prot.26585.

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