D-I-TASSER DIT6377

D-I-TASSER results for DIT6377

Input Sequence in FASTA format

>DHFR (159 residues)
MTLSILVAHDLQRVIGFENQLPWHLPNDLKHVKKLSTGHTLVMGRKTFESIGKPLPNRRN
VVLTSDTSFNVEGVDVIHSIEDIYQLPGHVFIFGGQTLFEEMIDKVDDMYITVIEGKFRG
DTFFPPYTFEDWEVASSVEGKLDEKNTIPHTFLHLIRKK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTLSILVAHDLQRVIGFENQLPWHLPNDLKHVKKLSTGHTLVMGRKTFESIGKPLPNRRNVVLTSDTSFNVEGVDVIHSIEDIYQLPGHVFIFGGQTLFEEMIDKVDDMYITVIEGKFRGDTFFPPYTFEDWEVASSVEGKLDEKNTIPHTFLHLIRKK
Prediction	CSSSSSSSSCCCCCSCCCCCCCCCCHHHHHHHHHHHCCCSSSSSCCHHHHCCCCCCCCSSSSSSCCCCCCCCCSSSSSCHHHHHHHCCCSSSSCCHHHHHHHHHHCCSSSSSSSCCCCCCCSSCCCCCHHHCSSSSSSSCCCCCCCCCCSSSSSSSSCC
Confidence	959999999289964289971762749999999985698399936715538887899859999368887899979990899998626967998469999999997999999997774365332899994656999998535677899646999999869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTLSILVAHDLQRVIGFENQLPWHLPNDLKHVKKLSTGHTLVMGRKTFESIGKPLPNRRNVVLTSDTSFNVEGVDVIHSIEDIYQLPGHVFIFGGQTLFEEMIDKVDDMYITVIEGKFRGDTFFPPYTFEDWEVASSVEGKLDEKNTIPHTFLHLIRKK
Prediction	440100000043310046450213146115303511443000102111420441256220000023451526302003124301620640000112200420052033010030465160002005134740531455635346746150312334458
	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                  80                 100                 120                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CSSSSSSSSCCCCCSCCCCCCCCCCHHHHHHHHHHHCCCSSSSSCCHHHHCCCCCCCCSSSSSSCCCCCCCCCSSSSSCHHHHHHHCCCSSSSCCHHHHHHHHHHCCSSSSSSSCCCCCCCSSCCCCCHHHCSSSSSSSCCCCCCCCCCSSSSSSSSCC
MTLSILVAHDLQRVIGFENQLPWHLPNDLKHVKKLSTGHTLVMGRKTFESIGKPLPNRRNVVLTSDTSFNVEGVDVIHSIEDIYQLPGHVFIFGGQTLFEEMIDKVDDMYITVIEGKFRGDTFFPPYTFEDWEVASSVEGKLDEKNTIPHTFLHLIRKK

3fl8A

0.42

12.38

1.50

DEthreader

MIVSFMVAMDENRVIGKDNNLPWRLPSELQYVKKTTMGHPLIMGRKNYEAIGRPLPGRRNIIVTRNEGYHVEGCEVAHSVEEVFECNEEIFIFGGAQIYDLFLPYVDKLYITKIHHAFEGDTFFPEMDMTNWKEVFVEKGLTDEKNPYTYYYHVYEKQQ

3fl8A

0.42

12.38

1.50

DEthreader

MIVSFMVAMDENRVIGKDNNLPWRLPSELQYVKKTTMGHPLIMGRKNYEAIGRPLPGRRNIIVTRNEGYHVEGCEVAHSVEEVFECNEEIFIFGGAQIYDLFLPYVDKLYITKIHHAFEGDTFFPEMDMTNWKEVFVEKGLTDEKNPYTYYYHVYEKQQ

3fyvX

1.00

0.99

27.82

2.94

SPARKS-K

-TLSILVAHDLQRVIGFENQLPWHLPNDLKHVKKLSTGHTLVMGRKTFESIGKPLPNRRNVVLTSDTSFNVEGVDVIHSIEDIYQLPGHVFIFGGQTLFEEMIDKVDDMYITVIEGKFRGDTFFPPYTFEDWEVASSVEGKLDEKNTIPHTFLHLIRKK

7rzoA

0.39

0.38

11.35

0.67

CEthreader

MKLSMIVALDRNRGIGQGNAMPWHLPDDFKHFKALTLGKPILMGRKTAESIGRVLPGRTNLVLTRSGQVPFEGMRAVASLDEAKTIASELCIIGGGEIFHQLLDQASDLYLTWVDAEIPADTHFPEVDMQDWREVSSEPHPADERHAYAFRFAHYVRR-

7yavB2

0.13

0.12

4.12

0.22

MUSTER

IITIISATFH-----GSRDRLLPLMQEEFPELG-LGKEDFKEMSWVQSIVHNYKDDDPLEVLLNKTVNFEPNPSDYVKKLEKLLARLYEFFPYGGTTRINNHLSWVRSVY----------DSMTPYVSKNPR-FRDLDIGVNPNESDTTSAYNYVKQAS

3fl8A

0.43

12.55

1.73

HHsearch

MIVSFMVAMDENRVIGKDNNLPWRLPSELQYVKKTTMGHPLIMGRKNYEAIGRPLPGRRNIIVTRNEGYHVEGCEVAHSVEEVFELCEEIFIFGGAQIYDLFLPYVDKLYITKIHHAFEGDTFFPEMDMTNWKEVFVEKGLTDEKNPYTYYYHVYEKQQ

3fl8A

0.43

12.55

2.67

FFAS-3D

MIVSFMVAMDENRVIGKDNNLPWRLPSELQYVKKTTMGHPLIMGRKNYEAIGRPLPGRRNIIVTRNEGYHVEGCEVAHSVEEVFELCEEIFIFGGAQIYDLFLPYVDKLYITKIHHAFEGDTFFPEMDMTNWKEVFVEKGLTDEKNPYTYYYHVYEKQQ

4q6aA

0.99

0.97

27.31

2.56

CNFpred

-TLSILVAHDLQRVIGFENQLPWHLPNDLKHLKKLSTGHTLVMGRKTFESIGKPLPNRRNVVLTSDTSFNVEGVDVIHSIEDIYQLPGHVFIFGGQTLYEEMIDKVDDMYITVIEGKFRGDTFFPPYTFEDWEVASSVEGKLDEKNTIPHTFLHLIRK-

4m7uA

0.46

13.39

1.50

DEthreader

GMLAAIWAQDEQGVIGKEGKLPWHLPNDLKFFKEKTIHNTLVLGRATFEGMGRPLPNRTTIVLTSNPDYQAEGVLVMHSVEEILAYYGVTVIGGGSVVFKELIPACDVLYRTMIHETFEGDTFFPEIDWSVWEKVATVPGVVDEKNLYAHDYETYHRN-

3ix9A

0.30

9.15

1.50

DEthreader

KKIVAIWAQDEEGVIGKDNRLPWYLPAELQHFKETTLNHAILMGRVTFDGMGRLLPKRETLILTRNPEEKIDGVATFHDVQSVLDWQKNLYIVGGKQIFQAFEPYLDEVIVTHIHARVEGTYFPAEFDLSLFETVSSKFYTKDEKNPYDFTIQYRKRKE

(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	0.87
	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.

References:
1.	Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.