I-TASSER results

I-TASSER results for job id Rv2516c

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

Input Sequence in FASTA format

>protein (267 residues)
MTADWVVTFTFDADPSMETMDAWETQLEGFDALVSRVPGHGIDVTVYAPGDWSVFDALAK
MAGEVMPVVQAKSPIAVQIISEPEHRLRAEAFTTPELMSAAEIADELGVSRQRVHQLRST
AGFPAPLADLRGGAVWDAAAVRRFAETWERKPGRPHTGTAKFAYSWAVGPAVGRSGKAPN
VRWRVENPDKIRFVLRNIGDDIAEDVEIDLSRIDAITRNVPKKTVIRPGEGLNMVLIAAW
GHPLPNQLYVRWAGQDEWAAVPLHPAH

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MTADWVVTFTFDADPSMETMDAWETQLEGFDALVSRVPGHGIDVTVYAPGDWSVFDALAKMAGEVMPVVQAKSPIAVQIISEPEHRLRAEAFTTPELMSAAEIADELGVSRQRVHQLRSTAGFPAPLADLRGGAVWDAAAVRRFAETWERKPGRPHTGTAKFAYSWAVGPAVGRSGKAPNVRWRVENPDKIRFVLRNIGDDIAEDVEIDLSRIDAITRNVPKKTVIRPGEGLNMVLIAAWGHPLPNQLYVRWAGQDEWAAVPLHPAH
Prediction	CCCCEEEEEEHCCCCCHHHHHHHHHHHCCCCCCEEEHCCCEEEEEEEHCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEHCCHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEHCCCCEEEEEEHCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCEEEEEHCCCCCCCHCCCCCCC
Conf.Score	997579999976887568899999985788764566478668999996787589999999999999887646775689864556665455677877789999999989858999999987999945543468876569999999999898899986589999999999999998578888647987688757999976888655799966886643334678888888876443456775588876799996788886555789999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MTADWVVTFTFDADPSMETMDAWETQLEGFDALVSRVPGHGIDVTVYAPGDWSVFDALAKMAGEVMPVVQAKSPIAVQIISEPEHRLRAEAFTTPELMSAAEIADELGVSRQRVHQLRSTAGFPAPLADLRGGAVWDAAAVRRFAETWERKPGRPHTGTAKFAYSWAVGPAVGRSGKAPNVRWRVENPDKIRFVLRNIGDDIAEDVEIDLSRIDAITRNVPKKTVIRPGEGLNMVLIAAWGHPLPNQLYVRWAGQDEWAAVPLHPAH
Prediction	753402020315442424314414460552322123336340302131454321142034105401411443433404424454234446514334011113005214023420340374661251134255241133630450166256644536553253145242452156355545141316445323110222344315404033742541255145742042342230112111444223301030344542121313578
	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

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

Sec.Str
Seq

CCCCEEEEEEHCCCCCHHHHHHHHHHHCCCCCCEEEHCCCEEEEEEEHCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEHCCHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEHCCCCEEEEEEHCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCEEEEEHCCCCCCCHCCCCCCC
MTADWVVTFTFDADPSMETMDAWETQLEGFDALVSRVPGHGIDVTVYAPGDWSVFDALAKMAGEVMPVVQAKSPIAVQIISEPEHRLRAEAFTTPELMSAAEIADELGVSRQRVHQLRSTAGFPAPLADLRGGAVWDAAAVRRFAETWERKPGRPHTGTAKFAYSWAVGPAVGRSGKAPNVRWRVENPDKIRFVLRNIGDDIAEDVEIDLSRIDAITRNVPKKTVIRPGEGLNMVLIAAWGHPLPNQLYVRWAGQDEWAAVPLHPAH

4bm5A

0.10

0.09

0.96

0.67

MUSTER

-SNLIDFYIRNGILEMENEQAVYPVNLRGVLNILQEMYRQYLIQSFAAKSRKERLFNNLAHLGNILGVNAIHSNIGSVIYKTYASQALTNNRLEEKDIELRNIQNMLSMDEATCRTLLQETK--EARAGFLFDKIFMAEAVAEFRRVCRELDVEDRRVRAFRAEIEHAIENSLLKESQEELGISAEKARQVLLDCIQDRCEALIVQAAASLRQRRQEGAARDLSRALRQELYLVYQAYALGTARSN-------AENDQVKLGIQAA-

5cwdA

0.07

0.04

0.64

0.58

dPPAS

-----------TKEDARSTCEKAARKAAESNDEEVAKQAAKDCLEVAKQAGMPTKEAARSFCEAAARAAAESNDEEVAKIAAKACLEVAKQAGMPTKEAARSFCEAAARAAAESNDEEVAKIAAKACLEVAKQAGMPTKEAARSFCEAAKRAAKESNDEEVEKIAKKACKEVAKQAGMPWLE-------------------------------------------------------------------------------------

1z4hA

0.12

0.03

0.25

0.54

wdPPAS

---------------------------------------------------------------------------------------MQHELQPDSLVDLKFIMADTGFGKTFIYDRIKSGDLPKAKV-IHGRARWLYRDHCEFKNKLLSRANG-----------------------------------------------------------------------------------------------------------------

4bm5A

0.13

0.12

0.88

0.63

wMUSTER

NLIDFYIR---GILEMENEQAVYPVNLRGLNILIQSFAAKS-------RTEKERLFNNLAHLGNILGVNAIHSNIGSVIYKTYASQALTNNRLEEKDI-LRNIQNMLSMDEATCRTLLQE----ARAGFLFDKIF-MAEAVAEFRRVCREDVEDRRVRAFRAEIEHAIENLLKESQEELGISAEKARQ-----VLLDCIQDRCEALSLRQRRQEGAARDLSRAL---RQELYLVYQAYALGTARSN-------AENDQVKLGIQAA-

4hkuA

0.14

0.08

0.55

0.69

wPPAS

-----------------------------------------------ARLSQEIILNAEKIIYEK------------------------EK------TTLYDIASNLNVTHAAL--------YRQKLAL-------WLEETSREIFAWTQDAGQTPDDALHDWLWLLADTKKKRYKTDRKFLLYTDYIEQNEELVKNHVAHLAQKAE-------EVSGRTNQGNAI-------ITAFTYFHNP----YFARWE-----------AGY

5cwdA

0.10

0.06

0.61

0.84

dPPAS2

-----------TKEDARSTCEKAARKAAESNDEEVAKQAAKDCLEVAKQAGMPTKEAARSFCEAAARAAAESNDEEVAKIAAKACLEVAKQAGMPTKEAAARAAAESNDEEVAKIAAKAC----LEVAKQAGMP---TKEAARSFCEAAKRAAKESNDEEVEKIAKKACKEVAKQAGMPWLE-------------------------------------------------------------------------------------

3tdvA

0.08

0.93

0.74

PPAS

--------------QNKLHYTTMIMTQDISIQSVESLGNGDWVFRFPKSQQGADELNKEIQLLPLLVGCVKVNIPQYVYIGKRSDGNVQGQILGEDGMAVFPDDAKDRLALQLAEFMNELSAFPVETAISAGVPVTNLKNKILLLSEAVEDQVFPLLDESLRDYLTLRFQSYMTHPVYTRYTPRLIHGDSPDHFLTNLNSRQTPLTGI--DCGELFTRQVMAYRGEVDLDTHIRKVSLFVTFDQVSYLLEGLRARDQDW---ISEGL

5dudB

0.12

0.09

0.72

0.69

Env-PPAS

LIGETAVVLELEPPVTLASQKRIWRLAQRMPNVVEAIPGNNITVILR-----NPESLALDAIERLQRWWEESERFIEIPV-------VYGGAGGPD---LAVVAAHCGLSEKQVVELHSSVEY--VVWFLGFQPGF------PYLGSLPEQLHTPR--------------------LVPAGSVGIG----GPQTGVYPLATPGGWQLIGHTSLSLFDPARDEPILLRPG------------------DSVRF------VPQK-----

5cwiA

0.10

0.09

0.86

0.66

MUSTER

-----------DIEKLCKKAESEAREARSKAEELRQRHPD----SQAARDAQKLASQAEEAVKLACELAQEHPNA-------DIAKLCIK---------AASEAAEAASKAAELAQRHPDSQAARDAIKLASQAAEAVKLACELAQEHPNADIAKLCIKAASEAAEAASKAAELAQRHPDSQAARDAIK----LASQAAEAVKLACELAQEHPNADIAKKCIKAASEAAEEASKAAEEAQRHPDSQKAIKEASQKAEEVKERCER--

3tdvA

0.10

0.09

0.95

0.55

dPPAS

--------------QNKLHYTTMIMTQFPDISIAILVNGDWVFRFPKSQQGADELNKEIQLLPLLVGCVKVNIPQYVYIGKRSDYRKVQGQILGEDGMAVFPDDAKDRLALQLAEFMNELSAFPVETAISAGVPVTNLKNKILLLSEAVEDQVFPLLDESLRDYLTLRFQSYMTHPVYTRYTPRLIHGDSPDHFLTNLNSRQTPLTGIIDFGDAAISDPDYDYVYLLEDCGELFTRQVMAYRGEVDDTHIRKVSLFVTFDQVSYLLE

(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=-5.00

Estimated TM-score = 0.21±0.05

Estimated RMSD = 18.7±2.2Å

Download Model 2

C-score=-5.00

Download Model 3

C-score=-4.99

Download Model 4

C-score=-5.00

Download Model 5

C-score=-5.00

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	5d06A	0.498	6.28	0.054	0.865
2	3ahxA	0.494	5.31	0.065	0.753
3	1v02E	0.492	5.25	0.056	0.745
4	3wh5A	0.492	5.35	0.065	0.749
5	3wq4A	0.491	5.36	0.040	0.753
6	2jf6B	0.490	5.38	0.052	0.753
7	3ptkA	0.490	5.33	0.056	0.749
8	5cg0A	0.490	5.35	0.056	0.749
9	3u57A	0.490	5.43	0.044	0.757
10	2dgaA	0.489	5.27	0.049	0.742

(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	0.09	4	5jrcC	CA	Rep, Mult	63,102,106
2	0.04	2	3c67A	GLC	Rep, Mult	114,115,116,117,118,123
3	0.04	2	3slpC	NUC	Rep, Mult	111,119
4	0.02	1	1xjmB	TTP	Rep, Mult	28,68
5	0.02	1	4ytrC	TGK	Rep, Mult	112,174
6	0.02	1	1pumA	UUU	Rep, Mult	123,126
7	0.02	1	3lv4A	CA	Rep, Mult	124,267
8	0.02	1	3iukA	MG	Rep, Mult	257,267
9	0.02	1	3my9A	MG	Rep, Mult	104,107
10	0.02	1	3ef2A	CA	Rep, Mult	12,14
11	0.02	1	1bjpA	OXP	Rep, Mult	123,131
12	0.02	1	3c67B	GLC	Rep, Mult	100,137,140,141,144
13	0.02	1	1r3nC	BIB	Rep, Mult	136,196,253,254
14	0.02	1	1jm0A	DMS	Rep, Mult	141,142,145,168
15	0.02	1	1brrC	ARC	Rep, Mult	145,164,168
16	0.02	1	3fwsB	MG	Rep, Mult	108,110,111
17	0.02	1	1jb0M	CLA	Rep, Mult	163,167
18	0.02	1	3osuA	MG	Rep, Mult	102,161

	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	1tr1D	0.486	5.36	0.065	0.749	3.2.1.21	NA
2	0.060	1bgaA	0.489	5.41	0.077	0.753	3.2.1.21	NA
3	0.060	1wcgA	0.485	5.31	0.049	0.745	3.2.1.147	NA
4	0.060	2dgaA	0.489	5.27	0.049	0.742	3.2.1.21	NA
5	0.060	2e3zA	0.489	5.35	0.056	0.753	3.2.1.21	NA
6	0.060	3gnrA	0.485	5.33	0.069	0.745	3.2.1.21	3
7	0.060	1qoxM	0.487	5.39	0.073	0.749	3.2.1.21	NA
8	0.060	2a3lA	0.479	5.47	0.048	0.760	3.5.4.6	NA
9	0.060	1wdpA	0.471	5.85	0.055	0.783	3.2.1.2	NA
10	0.060	1e1eB	0.480	5.78	0.071	0.779	3.2.1.21	NA
11	0.060	1np2A	0.488	5.36	0.069	0.749	3.2.1.21	NA
12	0.060	2jieA	0.483	5.32	0.057	0.745	3.2.1.21	NA
13	0.060	1b1yA	0.475	5.77	0.043	0.794	3.2.1.2	NA
14	0.060	2pbgA	0.482	5.53	0.045	0.749	3.2.1.85	NA
15	0.060	3cmjA	0.487	5.51	0.057	0.760	3.2.1.21	NA
16	0.060	3f4vA	0.481	5.48	0.044	0.753	3.2.1.21	NA
17	0.060	1myrA	0.482	5.58	0.037	0.753	3.2.1.147	NA
18	0.060	1od0B	0.487	5.31	0.073	0.745	3.2.1.21	NA
19	0.060	2jf6B	0.490	5.38	0.052	0.753	3.2.1.105	NA

(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	0.12	0.487	5.31	0.07	0.75	1od0B	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
1	0.07	0.482	5.53	0.04	0.75	2pbgA	GO:0004553 GO:0005975 GO:0005990 GO:0008152 GO:0016787 GO:0016798 GO:0019512 GO:0033920
2	0.07	0.488	5.33	0.06	0.75	3ta9A	GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
3	0.07	0.488	5.40	0.09	0.75	1gnxA	GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
4	0.07	0.488	5.36	0.07	0.75	1np2A	GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
5	0.07	0.486	5.43	0.07	0.75	3vifA	GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0102483
6	0.07	0.488	5.40	0.08	0.75	3ahyB	GO:0004553 GO:0005975 GO:0008422
7	0.07	0.485	5.48	0.06	0.76	4ha3A	GO:0004553 GO:0004565 GO:0005975 GO:0008152 GO:0016787 GO:0016798
8	0.07	0.487	5.31	0.04	0.74	4ipnE	GO:0004553 GO:0005975 GO:0008152 GO:0008706 GO:0016787 GO:0016798
9	0.07	0.478	5.25	0.07	0.74	3wdpP	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
10	0.07	0.469	5.86	0.06	0.77	1qvbA	GO:0004553 GO:0005975 GO:0008152 GO:0016798
11	0.07	0.487	5.39	0.07	0.75	1qoxA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
12	0.07	0.490	5.43	0.04	0.76	3u57A	GO:0004553 GO:0005975 GO:0008152 GO:0009820 GO:0009821 GO:0016740 GO:0016787 GO:0016798 GO:0050247 GO:0050506
13	0.07	0.478	5.40	0.04	0.74	5fooA	GO:0004553 GO:0005975
14	0.07	0.487	5.40	0.06	0.75	3w53A	GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483
15	0.07	0.485	5.39	0.07	0.75	3gnoA	GO:0004553 GO:0004565 GO:0005576 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0033907 GO:0042973 GO:0080079 GO:0080083 GO:0102483 GO:1901657
16	0.07	0.485	5.31	0.05	0.75	1wcgA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0019137 GO:0046872
17	0.07	0.489	5.35	0.06	0.75	2e3zA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0080079 GO:0102483
18	0.07	0.494	5.31	0.07	0.75	3ahxA	GO:0004553 GO:0005975 GO:0008152 GO:0008422 GO:0016787 GO:0016798 GO:0030245 GO:0102483

Consensus prediction of GO terms

Molecular Function	GO:0015926
GO-Score	0.57
Biological Processes	GO:0051275	GO:0030243
GO-Score	0.57	0.57
Cellular Component
GO-Score

(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.