I-TASSER results

I-TASSER results for job id Rv0481c

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Input Sequence in FASTA format

>protein (174 residues)
MPRSFDMSADYEGSVEEVHRAFYEADYWKARLAETPVDVATLESIRVGGDSGDDGTIEVV
TLQMVRSHNLPGLVTQLHRGDLSVRREETWGPVKEGIATASIAGSIVDAPVNLWGTAVLS
PIPESGGSRMTLQVTIQVRIPFIGGKLERLIGTQLSQLVTIEQRFTTLWITNNV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MPRSFDMSADYEGSVEEVHRAFYEADYWKARLAETPVDVATLESIRVGGDSGDDGTIEVVTLQMVRSHNLPGLVTQLHRGDLSVRREETWGPVKEGIATASIAGSIVDAPVNLWGTAVLSPIPESGGSRMTLQVTIQVRIPFIGGKLERLIGTQLSQLVTIEQRFTTLWITNNV
Prediction	CCCEEEEEEEHCCCHHHHHHHHCCHHHHHHHHHHHCCCCCEEEEEEHCCCCCCCCEEEEEEEEHCCHHHCHHHHHHHCCCCEEEEEEEEEEHCCCCEEEEEEEEEEHCCEEEEEEEEEEEHCCCCCEEEEEEEEEEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Conf.Score	996578999978999999999879999999999979988678889976777788789999999757766669999864797899999999865898899999999957558999999999678998689999999999975656899999999999999999999999999859
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MPRSFDMSADYEGSVEEVHRAFYEADYWKARLAETPVDVATLESIRVGGDSGDDGTIEVVTLQMVRSHNLPGLVTQLHRGDLSVRREETWGPVKEGIATASIAGSIVDAPVNLWGTAVLSPIPESGGSRMTLQVTIQVRIPFIGGKLERLIGTQLSQLVTIEQRFTTLWITNNV
Prediction	864525342516241430140023560044106616265241452415546456220302234404474015103513576151423340344663424040304044231404030303534755313130404040301011430053016303501540251045115738
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Normalized B-facotr

(B-factor is a value to indicate the extent of the inherent thermal mobility of residues/atoms in proteins. In I-TASSER, this value is deduced from threading template proteins from the PDB in combination with the sequence profiles derived from sequence databases. The reported B-factor profile in the figure below corresponds to the normalized B-factor of the target protein, defined by B=(B'-u)/s, where B' is the raw B-factor value, u and s are respectively the mean and standard deviation of the raw B-factors along the sequence. (Click here to read more about predicted normalized B-factor)

Top 10 threading templates used by I-TASSER

Rank

PDB
Hit

Iden1

Iden2

Cov

Norm.
Zscore

Download
Align.

                  20                  40                  60                  80                 100                 120                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCEEEEEEEHCCCHHHHHHHHCCHHHHHHHHHHHCCCCCEEEEEEHCCCCCCCCEEEEEEEEHCCHHHCHHHHHHHCCCCEEEEEEEEEEHCCCCEEEEEEEEEEHCCEEEEEEEEEEEHCCCCCEEEEEEEEEEEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
MPRSFDMSADYEGSVEEVHRAFYEADYWKARLAETPVDVATLESIRVGGDSGDDGTIEVVTLQMVRSHNLPGLVTQLHRGDLSVRREETWGPVKEGIATASIAGSIVDAPVNLWGTAVLSPIPESGGSRMTLQVTIQVRIPFIGGKLERLIGTQLSQLVTIEQRFTTLWITNNV

2ns9A

0.18

0.15

0.82

1.41

MUSTER

LKVRYEGSFEVSKTPEEVFEFLTDPKRFSRAF-------PGFKSVEVE-----DGSFTIELRLSLGP----------LR--GDARVRASFEDLEKPS-KATVKGSGRGAGSTLDFTLRFAVEPSGGGSRVSWVFEGNVGGLAMG-------GRVLDSLARRMINDVISGVKREL

2ns9A

0.20

0.17

0.83

1.59

dPPAS

LKVRYEGSFEVSKTPEEVFEFLTDPKRFSRAF-------PGFKSVEV-----EDGSFTIELRLSLGP----------LRGDARVRASFEDLEKPS---KATVKGSGRGAGSTLDFTLRFAVEPSGGGSRVSWVFEGNVGGLMGGRVLDSLARRMINDVISGVKRELGEA-----

2ns9A

0.20

0.17

0.83

1.91

wdPPAS

LKVRYEGSFEVSKTPEEVFEFLTD-------PKRFSRAFPGFKSVEVE-----DGSFTIELRLSLGP----------LRGDARVRASFEDLEKPS---KATVKGSGRGAGSTLDFTLRFAVEPSGGGSRVSWVFEGNVGGLMGGRVLDSLARRMINDVISGVKRELGE--A---

2ns9A

0.18

0.15

0.83

1.75

wMUSTER

LKVRYEGSFEVSKTPEEVFEFLTDPKRFSRAF-------PGFKSVEVE-----DGSFTIELRLSLGP----------LR--GDARVRASFEDLEKPS-KATVKGSGRGAGSTLDFTLRFAVEPSGGGSRVSWVFEGNVGGLAMGRVLDSLARRMINDVISGVKRELGE--A---

2ns9A

0.21

0.17

0.79

1.76

wPPAS

LKVRYEGSFEVSKTPEEVFEFLTD----PKRFSRA------FKSVEVE-----DGSFTIELRLSLG----P--LRGDARVRASFEDLE----------KATVKGSGRGAGSTLDFTLRFAVEPSGGGSRVSWVFEGNVGGLAMGRVLDSLARRMINDVISGVKRELGE--A---

2ns9A

0.21

0.17

0.81

3.80

dPPAS2

LKVRYEGSFEVSKTPEEVFEFLTD----PKRFSRA---FPGFKSVEV-----EDGSFTIELRLSLGP----------LRGDARVRASFEDLEKPS---KATVKGSGRGAGSTLDFTLRFAVEPSGGGSRVSWVFEGNVGGLAMGRVLDSLARRMINDVISGVKREL--------

2ns9A

0.21

0.17

0.82

1.61

PPAS

LKVRYEGSFEVSKTPEEVFEFLTDPKRFSRAF---------FKSVEVE-----DGSFTIELRLSLG----P------LRGDARVRASFEDLEKPS---KATVKGSGRGAGSTLDFTLRFAVEPSGGGSRVSWVFEGNVGGLAMGRVLDSLARRMINDVISGVKRELGEA-----

3p9vA

0.11

0.10

0.86

1.55

Env-PPAS

VSIELNRDLEIPASYDEVFDLLAD-------VPKSASHFPKVDKLVDLG----NNAYRWEEKVGVDKHAI----------QSVYACTYHADK-EAGKITWSPIKGEG--NGVVSGSWTLSAKGDN-ATAVKFQTSAELTVPLPSLAISPVIKHEFNSLVDTYANLKKAFLEHHH

2pcsA

0.17

0.14

0.84

1.40

MUSTER

L--NGNGSIELKGTVEEVWSKLMDPSILSKCI-------MGCKSLELIG----EDKYKADLQIGI------AAVKGKYDAIIEVTDIKP-----PYHYKLLVNGEGGPGFVNAEGVIDLTPINDE-CTQLTYTYSAEVGGKVIGQ---RMLGGVAKLLISDFFKKIQKEIAKSH

2d4rA

0.19

0.16

0.83

1.41

dPPAS

--PEVRAERYIPAPPERVYRLAKD-------LEGLKPYLKEVESLEVVAREGARTRSRWVAVA---------------GKKVRWLEEEEWDDENL----RNRFFSPEGDFDRYEGTWVFLPE--GEGTRVVLTLTYELTIPIFGGLLRKLVQKLQENVESLLKGLEERVLAASS

(a)	Iden1 is the number of template residues identical to query divided by number of aligned residues.
(b)	Iden2 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.
(e)	Download Align. list the threading program used to identify the template provide the 3D structure of aligned regions of threading templates.

Top 5 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of higher value signifies a model with a high confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.)

More about C-score

Local structure accuracy of first model

Download Model 1

C-score=-0.41

Estimated TM-score = 0.66±0.13

Estimated RMSD = 5.9±3.7Å

Download Model 2

C-score=-2.72

Download Model 3

C-score=-0.60

Download Model 4

C-score=-2.27

Download Model 5

C-score=-3.38

Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)

Top 10 Identified stuctural analogs in PDB

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov
1	2ns9A	0.755	1.78	0.208	0.828
2	2pcsA	0.721	2.18	0.123	0.833
3	3q64A	0.707	2.70	0.096	0.839
4	3tfzA	0.706	2.58	0.054	0.856
5	2e3mA	0.698	2.96	0.071	0.879
6	2mouA	0.698	3.05	0.089	0.902
7	3kdhA	0.695	2.58	0.088	0.845
8	4xrtA2	0.693	2.64	0.122	0.845
9	3oquA	0.692	2.61	0.088	0.845
10	1jssA	0.687	2.70	0.101	0.851

(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 function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)

Ligand binding sites

Rank	C-score	Cluster size	PDB Hit	Lig Name	Download Complex	Ligand Binding Site Residues
1	0.15	18	4n3eB	2AN	Rep, Mult	7,9,11,18,22,119,130,132,158,159,162
2	0.08	10	3nmnA	PYV	Rep, Mult	59,84,86,102,104,113,115,150,154,155
3	0.07	9	4qipA	SDS	Rep, Mult	9,57,59,86,100,119,156,159,160
4	0.04	5	4a81A	2AN	Rep, Mult	7,9,102,119,132,134,152,155,156,159,160
5	0.03	4	3gb4A	D3M	Rep, Mult	70,100,102,115,117,151,154
6	0.02	2	1bv10	III	Rep, Mult	20,24,28,29,32,33,45,46,47,48,91,93
7	0.02	3	3nj1A	PYV	Rep, Mult	40,41,59,61,63,84,86,113,115,154,155
8	0.02	2	4ryvA	ZEA	Rep, Mult	5,7,134,136,151,152,155
9	0.01	1	3ojiA	PYV	Rep, Mult	40,41,60,77,79,83,85,111,113,150
10	0.01	1	1fipA	III	Rep, Mult	141,143
11	0.01	1	3arcJ	III	Rep, Mult	169,170
12	0.01	1	1txcA	2AN	Rep, Mult	159,162,163,166
13	0.01	1	3sxnD	COA	Rep, Mult	81,82
14	0.01	1	2flhC	ZEA	Rep, Mult	22,28,59,84,86,102,119,158
15	0.01	1	1kj4B	III	Rep, Mult	110,111
16	0.01	1	2ns90	III	Rep, Mult	1,2,3,4,5,6,7,8,132,137,142,144,145,146,147,148,152,155,156
17	0.01	1	1y66A	DIO	Rep, Mult	151,155

	Download the all possible binding ligands and detailed prediction summary.
	Download the templates clustering results.
(a)	C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)	Cluster size is the total number of templates in a cluster.
(c)	Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)	Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column. Mult is the complex structures with all potential binding ligands in the cluster.

Enzyme Commission (EC) numbers and active sites

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov	EC Number	Active Site Residues
1	0.179	2vq5A	0.649	3.27	0.095	0.845	4.2.1.78	32,52,55
2	0.060	1eg9A	0.569	4.10	0.054	0.839	1.14.12.12	NA
3	0.060	1n63B	0.512	4.54	0.051	0.764	1.2.99.2	NA
4	0.060	2pmgB	0.328	5.29	0.034	0.575	5.4.2.2	74,80
5	0.060	1t3qB	0.499	4.73	0.077	0.759	1.3.99.17	NA
6	0.060	2fy3A	0.453	5.13	0.058	0.776	2.3.1.6	NA
7	0.060	1sczA	0.450	4.92	0.051	0.741	2.3.1.61	NA
8	0.060	1qaxA	0.477	4.16	0.042	0.690	1.1.1.88	16
9	0.060	1ciaA	0.449	4.81	0.065	0.724	2.3.1.28	163
10	0.060	1rm6A	0.443	5.18	0.095	0.764	1.3.99.20	NA
11	0.060	2q6bA	0.455	4.18	0.042	0.678	1.1.1.34	NA
12	0.060	1ygaA	0.465	4.69	0.044	0.713	5.1.3.3	NA
13	0.060	3en1A	0.569	4.02	0.111	0.822	1.14.12.11	NA
14	0.060	1im0A	0.529	4.68	0.045	0.799	3.1.1.32,3.1.1.4	115
15	0.060	2ihwA	0.468	4.71	0.076	0.753	2.3.1.168	NA
16	0.060	1dgjA	0.484	4.60	0.085	0.741	1.2.-.-	NA
17	0.060	2cf2C	0.455	4.74	0.054	0.678	2.3.1.85	108
18	0.060	1uliC	0.559	4.23	0.110	0.828	1.14.12.18	NA
19	0.060	3claA	0.450	4.88	0.065	0.730	2.3.1.28	4
20	0.060	1b5sE	0.467	4.84	0.068	0.759	2.3.1.12	18,117,119,132

(a)	Cscore^EC is the confidence score for the 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.

Gene Ontology (GO) terms

Rank	Cscore^GO	TM-score	RMSD^a	IDEN^a	Cov	PDB Hit	Associated GO Terms
Homologous GO templates in PDB
0	0.22	0.695	2.58	0.09	0.84	3kdhA	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
1	0.22	0.663	3.18	0.11	0.85	1ifvA	GO:0006952 GO:0009607 GO:0016787
2	0.21	0.678	3.00	0.09	0.84	3ojiB	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
3	0.21	0.677	3.12	0.07	0.86	3k3kA	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042802 GO:0042803 GO:0043086 GO:0080163
4	0.21	0.678	2.79	0.10	0.84	3nefA	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
5	0.21	0.654	3.14	0.12	0.82	1z94B	GO:0006950
6	0.21	0.672	3.27	0.09	0.86	5c9yA	GO:0006952 GO:0009607
7	0.21	0.688	2.60	0.10	0.84	3w9rA	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
8	0.21	0.663	2.96	0.07	0.83	4igvA	GO:0006952 GO:0009607 GO:0016068
9	0.20	0.717	2.74	0.09	0.86	3q64A	GO:0006950
10	0.19	0.684	2.79	0.11	0.85	2rerA	GO:0003824 GO:0008152 GO:0008168 GO:0008171 GO:0016740 GO:0017000 GO:0032259
11	0.19	0.679	2.78	0.06	0.82	4n0gC	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
12	0.19	0.663	3.08	0.08	0.84	2qimA	GO:0006952 GO:0009607 GO:0046872
13	0.19	0.651	2.75	0.08	0.78	3rd6A	GO:0006950
14	0.18	0.572	2.35	0.12	0.66	2q3qA	GO:0006952 GO:0009607
15	0.18	0.640	3.50	0.11	0.85	4m9bA	GO:0006952 GO:0009607
16	0.18	0.698	2.92	0.10	0.86	3putB	GO:0006950
17	0.17	0.686	3.24	0.07	0.87	4a80A	GO:0005737 GO:0006952 GO:0009607
18	0.17	0.673	2.99	0.07	0.84	2flhB	GO:0006952 GO:0009607
19	0.17	0.664	3.49	0.09	0.86	4c94A	GO:0006952 GO:0009607
20	0.16	0.689	2.64	0.10	0.85	3rt0C	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0042803 GO:0043086 GO:0080163
21	0.15	0.685	2.90	0.09	0.84	3otlA	GO:0006950
22	0.14	0.624	2.89	0.10	0.79	3cnwA	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0009738 GO:0010427 GO:0043086 GO:0080163
23	0.13	0.675	2.67	0.08	0.83	4oicA	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0009738 GO:0010427 GO:0043086 GO:0080163
24	0.12	0.696	2.84	0.04	0.88	1em2A	GO:0005737 GO:0005739 GO:0005765 GO:0005768 GO:0006629 GO:0006694 GO:0006701 GO:0006810 GO:0006839 GO:0006869 GO:0008202 GO:0008203 GO:0008289 GO:0015485 GO:0016020 GO:0016021 GO:0031902
25	0.11	0.698	3.05	0.09	0.90	2mouA	GO:0006810 GO:0006869 GO:0008289
26	0.11	0.622	2.60	0.10	0.76	4jdlB	GO:0004864 GO:0004872 GO:0005634 GO:0005737 GO:0005886 GO:0009738 GO:0010427 GO:0016020 GO:0043086 GO:0080163
27	0.10	0.698	2.96	0.07	0.88	2e3mA	GO:0000902 GO:0001701 GO:0003007 GO:0004672 GO:0005654 GO:0005737 GO:0005739 GO:0005783 GO:0005789 GO:0005794 GO:0005829 GO:0006468 GO:0006672 GO:0006810 GO:0006869 GO:0006936 GO:0006955 GO:0007029 GO:0007165 GO:0008283 GO:0008289 GO:0016301 GO:0016310 GO:0030148 GO:0034976 GO:0035620 GO:0035621 GO:0048471 GO:0055088 GO:0070273 GO:0070584 GO:0097001
28	0.10	0.674	3.21	0.09	0.86	5i8fA	GO:0006952 GO:0009607
29	0.10	0.685	2.83	0.07	0.87	2r55A	GO:0005829 GO:0006700 GO:0006810 GO:0006869 GO:0008289 GO:0032052
30	0.10	0.691	2.68	0.10	0.85	5brlA	GO:0005739 GO:0005783 GO:0005829 GO:0006810 GO:0006869 GO:0008289 GO:0015485 GO:0016023 GO:0034435
31	0.10	0.667	3.17	0.08	0.85	1tw0A	GO:0006952 GO:0009607
32	0.10	0.650	3.29	0.10	0.83	2il5A	GO:0006950
33	0.09	0.539	3.45	0.05	0.70	2i9yA	GO:0006952 GO:0009607

Consensus prediction of GO terms

Molecular Function	GO:0010427	GO:0042803	GO:0004864	GO:0004872	GO:0003824
GO-Score	0.62	0.62	0.62	0.62	0.31
Biological Processes	GO:0043086	GO:0080163	GO:0009738	GO:0006950
GO-Score	0.62	0.62	0.62	0.44
Cellular Component	GO:0005737	GO:0005634	GO:0005886
GO-Score	0.62	0.62	0.62

(a)	Cscore^GO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(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.
(f)	The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on Cscore^GO of the template.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Please cite the following articles when you use the I-TASSER server:
1.	J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2.	J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.	A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.	Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.