I-TASSER results

I-TASSER results for job id Rv2826c

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

Input Sequence in FASTA format

>protein (294 residues)
MAGLTRALVARHALGRAEAYDAALLDVAQDHLLYLLSQTVQFGDNRLVFKGGTSLRKCRL
GNVGRFSTDLDFSAPDDEVVLEVCELIDGARVGGFEFGVQSTRGDGRHWQLRVRHTELGE
PRIVASVEFARRPLALPSELLAFIQLPIHKAYGFGLPTLPVVAEAEACAEKLARYRRVAL
ARDLYDLNHFASRTIDEPLVRRLWVLKVWGDVVDDRRGTRPLRVEDVLAARSEHDFQPDS
IGVLTRPVAMAAWEARVRKRFAFLTDLDADEQRWAACDERHRREVENALAVLRS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| MAGLTRALVARHALGRAEAYDAALLDVAQDHLLYLLSQTVQFGDNRLVFKGGTSLRKCRLGNVGRFSTDLDFSAPDDEVVLEVCELIDGARVGGFEFGVQSTRGDGRHWQLRVRHTELGEPRIVASVEFARRPLALPSELLAFIQLPIHKAYGFGLPTLPVVAEAEACAEKLARYRRVALARDLYDLNHFASRTIDEPLVRRLWVLKVWGDVVDDRRGTRPLRVEDVLAARSEHDFQPDSIGVLTRPVAMAAWEARVRKRFAFLTDLDADEQRWAACDERHRREVENALAVLRS
Prediction	CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEHCCCEEEHHHCCCCCCCCCCEHCCCCCCCCHHHHHHHHHHHHHCCEEEEEEHCCCCCEEEEEEEEHCCCCCCEEEEEEEEHCCCCCCCCEEEHCCCCCCCCCCCCCCCCCEEEEHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHCCHHHHHHHHHHHHHHHC
Conf.Score	887999999998776577645788999999999999975656677579867744445544788887754556778886489999999999875646777645687558999998567888768999997567666764444444566444567777654566588999999999997888755679999999889975899999999875545654455478999999985655456666665567765445667777766777767875677776555677889999998759
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| MAGLTRALVARHALGRAEAYDAALLDVAQDHLLYLLSQTVQFGDNRLVFKGGTSLRKCRLGNVGRFSTDLDFSAPDDEVVLEVCELIDGARVGGFEFGVQSTRGDGRHWQLRVRHTELGEPRIVASVEFARRPLALPSELLAFIQLPIHKAYGFGLPTLPVVAEAEACAEKLARYRRVALARDLYDLNHFASRTIDEPLVRRLWVLKVWGDVVDDRRGTRPLRVEDVLAARSEHDFQPDSIGVLTRPVAMAAWEARVRKRFAFLTDLDADEQRWAACDERHRREVENALAVLRS
Prediction	744124411442335464534212231024100200143432344301020110012021373311010011315575236403510430322225133544563444030204445456421203020363233432533422532214314242130302303310020020024233000000000014462626133114004312542454355444314411552554513540241043533352334312441410240365453125156443540440142048
	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                 180                 200                 220                 240                 260                 280

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEHCCCEEEHHHCCCCCCCCCCEHCCCCCCCCHHHHHHHHHHHHHCCEEEEEEHCCCCCEEEEEEEEHCCCCCCEEEEEEEEHCCCCCCCCEEEHCCCCCCCCCCCCCCCCCEEEEHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHCCHHHHHHHHHHHHHHHC
MAGLTRALVARHALGRAEAYDAALLDVAQDHLLYLLSQTVQFGDNRLVFKGGTSLRKCRLGNVGRFSTDLDFSAPDDEVVLEVCELIDGARVGGFEFGVQSTRGDGRHWQLRVRHTELGEPRIVASVEFARRPLALPSELLAFIQLPIHKAYGFGLPTLPVVAEAEACAEKLARYRRVALARDLYDLNHFASRTIDEPLVRRLWVLKVWGDVVDDRRGTRPLRVEDVLAARSEHDFQPDSIGVLTRPVAMAAWEARVRKRFAFLTDLDADEQRWAACDERHRREVENALAVLRS

4ok0A

0.14

0.11

0.75

1.52

MUSTER

---------------------LSEQALNHEKLMRAIVKN--LADTPMVLKGETALYLGY--GLNRFSEDLDFDCHKKINLLGRVKSAIPNGIILNDIHIKKDTDSVGRYMVRYATKD-NKEEQTLKLEISYRDAPKESEVNVIE-------------GMRIAKIERIIDNKLCACFDRTKARDLFDLHFLAKHYEEHFNLDLASRLKDFSK----DPDKLVSDYLVDVKLDA----------LLNQIMDLEETALELGVMAQLIHKKLEKLEHH--------------------

4ok0A

0.16

0.12

0.75

1.81

dPPAS

---------------------LSEQALNHEKLMRAIVKN--LADTPMVLKGETALYLGY--GLNRFSEDLDFDCHKKINLLGRVKSAIPNGIILNDIHIKKDTDSVGRYMVRYATKD-NKEEQTLKLEISYRDAPKESEVNVIE-------------GMRIAKIERIIDNKLCACFDRTKARDLFDLHFLAKHY---EEHFNLDLASRLKDFSKDPDKLVSDYLVDVKLDALLNQIMDLEETA-------LELGVMAQLIHKKLEKLEHH------------------------

4ok0A

0.16

0.12

0.75

3.50

wdPPAS

---------------------LSEQALNHEKLMRAIVKNLA--DTPMVLKGETALYLGY--GLNRFSEDLDFDCHKKINLLGRVKSAIPNGIILNDIHIKKDTDSVGRYMVRYATKD-NKEEQTLKLEISYRDAPKESEVNVIE-------------GMRIAKIERIIDNKLCACFDGTKARDLFDLHFLAKHYEEHFNLDLASRLKDFSK-------DPDKLVSDYLVDVKLDALLNQIMDL---EETALELGVMAQLIHKKLEKLEHH------------------------

4ok0A

0.16

0.12

0.75

1.87

wMUSTER

---------------------LSEQALNHEKLMRAIVKN--LADTPMVLKGETALYLGY--GLNRFSEDLDFDCHKKINLLGRVKSAIPNGIILNDIHIKKDTDSVGRYMVRYATK-DNKEEQTLKLEISYRDAPKESEVNVIE-------------GMRIAKIERIIDNKLCACFDRTKARDLFDLHFLAKHYEEHFNLDLASRLKDFSK-------DPDKLVSDYLVDVKLDALLNQIMDL---EETALELGVMAQLIHKKLEKLEHH------------------------

4ok0A

0.16

0.12

0.75

3.81

wPPAS

---------------------LSEQALNHEKLMRAIVKNLA--DTPMVLKGETALYLGY--GLNRFSEDLDFDCHKKINLLGRVKSAIPNGIILNDIHIKKDTDSVGRYMVRYATKD-NKEEQTLKLEISYRDAPKESEVNVI-------------EGMRIAKIERIIDNKLCACFDRTKARDLFDLHFLAKHYEEHFNLDLASRLKDFSK-------DPDKLVSDYLVDVKLDALLNQIMDL---EETALELGVMAQLIHKKLEKLEHH------------------------

4ok0A

0.16

0.12

0.75

4.77

dPPAS2

---------------------LSEQALNHEKLMRAIVKN--LADTPMVLKGETALYLGY--GLNRFSEDLDFDCHKKINLLGRVKSAIPNGIILNDIHIKKDTDSVGRYMVRYATKD-NKEEQTLKLEISYRDAPKESEVNVIE-------------GMRIAKIERIIDNKLCACFDRTKARDLFDLHFLAKHYEEHFNLDLASRLKDFSK-------DPDKLVSDYLVDVKLDALLNQ---IMDLEETALELGVMAQLIHKKLEKLEHH------------------------

4ok0A

0.16

0.12

0.75

2.67

PPAS

---------------------LSEQALNHEKLMRAIVKN--LADTPMVLKGETALYLGY--GLNRFSEDLDFDCHKKINLLGRVKSAIPNGIILNDIHIKKDTDSVGRYMVRYATKD-NKEEQTLKLEISYRDAPKESEVNVI-------------EGMRIAKIERIIDNKLCACFDRTKARDLFDLHFLAKHYEEHFNLDLASRLKDFSK-------DPDKLVSDYLVDVKLDALLNQ---IMDLEETALELGVMAQLIHKKLEKLEHH------------------------

4ok0A

0.17

0.13

0.75

3.06

Env-PPAS

---------------------LSEQALNHEKLMRAIVKN--LADTPMVLKGETALYLGY--GLNRFSEDLDFDCHKKINLLGRVKSAIPNGIILNDIHIKKDTDSVGRYMVRYATKDNKE-EQTLKLEISYRDAPKESEVNVI-------------EGMRIAKIERIIDNKLCACFDRTKARDLFDLHFLAKHYEEHFNLDLASRLKDFSK-------DPDKLVSDYLVDVKLDALLNQ---IMDLEETALELGVMAQLIHKKLEKLEHH------------------------

4yxzA

0.09

0.91

0.72

MUSTER

ISVEELLKLAKAAYYSGTT---VEEAYKLALKLGISVEE-----------LLKLAEAAYYSGTT-VEEAYKLALKLGISVEELLKLAKAAYYSGTTVLALKLGISVEELLKLAKAAYYSGTTVEEAYKLALKLGISVEELLKLAEAAYYSGTTVEEAYKLAISVEELLKLAKAAYYSGTTVEEAYKLALKLGIS-----VEELLKLAKAAYYSGT---TVEEAYKLALKLGISVEELLKLAEAAYYSGTTVEEAYKLALKLGIVEELLKLAKAAYYSGTTVEEAYKLALKL---

4ok0A1

0.18

0.07

0.42

0.91

dPPAS

---------------------LSEQALNHEKLMRAIVKN--LADTPMVLKGETALYLGY--GLNRFSEDLDFDCHKKINLLGRVKSAIPNGIILNDIHIKKDTDSVGRYMVRYATKDNKE-EQTLKLEISYRDAPKESEVNVIEGMRIA-------------------------------------------------------------------------------------------------------------------------------------------------

(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=-1.26

Estimated TM-score = 0.56±0.15

Estimated RMSD = 9.0±4.6Å

Download Model 2

C-score=-1.77

Download Model 3

C-score=-2.22

Download Model 4

C-score=-2.17

Download Model 5

C-score=-2.19

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	4ok0A	0.724	1.28	0.163	0.752
2	4wseA	0.466	4.44	0.056	0.612
3	2yheA	0.453	6.27	0.084	0.758
4	4nurA	0.450	6.01	0.069	0.742
5	2cg2A	0.448	6.23	0.046	0.748
6	1oa0A	0.446	6.22	0.063	0.745
7	4pdxA1	0.440	6.07	0.074	0.711
8	2gafD	0.439	4.65	0.060	0.599
9	4p37A	0.437	4.96	0.065	0.612
10	1gntA	0.436	6.11	0.043	0.735

(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	0.35	17	3e0dA	CA	Rep, Mult	69,71
2	0.08	4	4xjeA	AMP	Rep, Mult	51,52,69,71,170,171,174,177,183
3	0.02	1	4wh5A	3QB	Rep, Mult	50,51,52,73,130,139,140,162,166,167,170,172
4	0.02	1	5cfuA	POP	Rep, Mult	52,65,67,68,69,71,182,183
5	0.02	1	3q2vA	MAN	Rep, Mult	69,126
6	0.02	1	3ercC	U	Rep, Mult	168,171,174,183

	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	0.060	2ri9B	0.405	6.30	0.051	0.670	3.2.1.113	NA
2	0.060	2vn7A	0.405	6.26	0.053	0.684	3.2.1.3	209
3	0.060	1zedA	0.390	6.25	0.038	0.660	3.1.3.1	174
4	0.060	3e2dA	0.398	6.43	0.043	0.697	3.1.3.1	182
5	0.060	1jqoA	0.409	6.48	0.058	0.701	4.1.1.31	NA
6	0.060	1hcuB	0.404	6.36	0.030	0.680	3.2.1.113	59
7	0.060	1kb0A	0.396	6.75	0.053	0.721	1.1.99.-	71
8	0.060	2gafD	0.439	4.65	0.060	0.599	2.7.7.19	71
9	0.060	1ut9A	0.398	6.57	0.039	0.691	3.2.1.4	NA
10	0.060	2eabA	0.412	6.34	0.053	0.697	3.2.1.63	NA
11	0.060	2qnoA	0.411	6.33	0.050	0.694	3.2.1.4	NA
12	0.060	3f2bA	0.416	5.64	0.046	0.633	2.7.7.7	142
13	0.060	2epoA	0.397	6.62	0.071	0.714	3.2.1.52	196,197
14	0.060	1tazA	0.403	5.67	0.051	0.636	3.1.4.17	186
15	0.060	3hsiB	0.396	6.36	0.040	0.667	2.7.8.8	NA
16	0.060	1h54B	0.409	5.72	0.051	0.639	2.4.1.8	NA
17	0.060	2zzgA	0.410	5.76	0.060	0.660	6.1.1.7	NA
18	0.060	1l2aE	0.429	6.07	0.057	0.694	3.2.1.4	NA
19	0.060	1jqnA	0.417	6.72	0.067	0.742	4.1.1.31	177

(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	0.07	0.450	6.01	0.07	0.74	4nurA	GO:0046872 GO:0046983
1	0.07	0.446	6.15	0.04	0.74	4pdxA	GO:0016787 GO:0018741 GO:0030288 GO:0046983
2	0.07	0.447	6.11	0.06	0.74	5aijA	GO:0016787 GO:0042802 GO:0046872 GO:0046983
3	0.07	0.466	4.44	0.06	0.61	4wseA	GO:0000166 GO:0004652 GO:0005524 GO:0006351 GO:0006397 GO:0016740 GO:0019012
4	0.07	0.453	6.27	0.08	0.76	2yheA	GO:0046872 GO:0046983
5	0.06	0.354	6.14	0.03	0.58	3lvzB	GO:0046872
6	0.06	0.279	7.05	0.07	0.53	1td9D	GO:0005737 GO:0006085 GO:0008152 GO:0008959 GO:0016407 GO:0016740 GO:0016746
7	0.06	0.357	5.34	0.10	0.53	3faiA	GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
8	0.06	0.286	6.71	0.04	0.51	3eoeD	GO:0000287 GO:0003824 GO:0004743 GO:0006096 GO:0016301 GO:0016310 GO:0016740 GO:0030955
9	0.06	0.327	5.88	0.05	0.52	3adrA	GO:0008270 GO:0046872
10	0.06	0.325	6.39	0.07	0.56	4awyB	GO:0046872
11	0.06	0.302	5.69	0.07	0.48	2zwrB	GO:0046872
12	0.06	0.317	6.50	0.04	0.54	3kzwA	GO:0004177 GO:0005622 GO:0005737 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0019538 GO:0030145 GO:0046872
13	0.06	0.306	5.85	0.03	0.48	2m5cA	GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
14	0.06	0.282	6.39	0.03	0.49	4ilsA	GO:0003824 GO:0006522 GO:0008784 GO:0016853 GO:0030170 GO:0030632
15	0.06	0.304	6.01	0.03	0.48	3zwfA	GO:0004518 GO:0004519 GO:0005634 GO:0005737 GO:0005829 GO:0008033 GO:0016787 GO:0016891 GO:0034414 GO:0042779 GO:0042781 GO:0046872 GO:0090502
16	0.06	0.314	6.47	0.05	0.54	2j3lB	GO:0000166 GO:0002161 GO:0004812 GO:0004827 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006433 GO:0006450 GO:0016874
17	0.06	0.291	6.47	0.04	0.50	2i7tA	GO:0000398 GO:0003723 GO:0004518 GO:0004519 GO:0004521 GO:0005634 GO:0005654 GO:0005847 GO:0006369 GO:0006378 GO:0006379 GO:0006397 GO:0006398 GO:0006406 GO:0008409 GO:0016787 GO:0030529 GO:0031124 GO:0046872 GO:0090305 GO:0090502
18	0.06	0.332	6.02	0.04	0.55	3jyhA	GO:0004177 GO:0004185 GO:0005576 GO:0005764 GO:0005794 GO:0005829 GO:0006508 GO:0008233 GO:0008236 GO:0008239 GO:0016023 GO:0016787 GO:0031410 GO:0031982 GO:0043231 GO:0070062

Consensus prediction of GO terms

Molecular Function	GO:0005515	GO:0043169
GO-Score	0.47	0.37
Biological Processes	GO:0006351	GO:0006397
GO-Score	0.07	0.07
Cellular Component	GO:0030288	GO:0019012
GO-Score	0.07	0.07

(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.