GPCR Sequence:

>tr|D3DT66|D3DT66_HUMAN Endothelial differentiation, sphingolipid G-protein-coupled receptor, 1, isoform CRA_a OS=Homo sapiens GN=EDG1 PE=3 SV=1
MGPTSVPLVKAHRSSVSDYVNYDIIVRHYNYTGKLNISADKENSIKLTSVVFILICCFII
LENIFVLLTIWKTKKFHRPMYYFIGNLALSDLLAGVAYTANLLLSGATTYKLTPAQWFLR
EGSMFVALSASVFSLLAIAIERYITMLKMKLHNGSNNFRLFLLISACWVISLILGGLPIM
GWNCISALSSCSTVLPLYHKHYILFCTTVFTLLLLSIVILYCRIYSLVRTRSRRLTFRKN
ISKASRSSEKSLALLKTVIIVLSVFIACWAPLFILLLLDVGCKVKTCDILFRAEYFLVLA
VLNSGTNPIIYTLTNKEMRRAFIRIMSCCKCPSGDSAGKFKRPIIAGMEFSRSKSDNSSH
PQKDEGDNPETIMSSGNVNSSS

Estimation of the GPCR-I-TASSER model for D3DT66

C-score = -0.070
TM-score = 0.700 (estimated)
RMSD = 6.9 A (estimated)

Here, C-score is a confidence score of the GPCR-I-TASSER predictions which is typically in [-5,2]. TM-score and RMSD measure how close the model is to the native structure and both are estimated based on the C-score. TM-score is in [0,1] with a value >0.5 implying the model of correct topology. The TM-score and RMSD estimations are made only for the first model because absolute values of TM-score and RMSD for the lower-rank models do not strongly correlate with the C-score. The models are ranked based on the structure density of GPCR-I-TASSER simulations.

The top ten threading templates used by GPCR-I-TASSER

Rank	PDB ID	Z-score	Download Templates
1	3emlA1	2.263	template1
2	2rh1_A	6.341	template2
3	1l9ha	2.267	template3
4	2z73a	5.447	template4
5	1l9ha	3.389	template5
6	2ks9A	3.238	template6
7	2rh1_A	5.168	template7
8	hs1u19	2.881	template8
9	2z73a	5.642	template9
10	2ks9A	2.043	template10
(a) Rank of templates represents the top ten threading templates used by GPCR-I-TASSER. (b) Z-score is the normalized Z-score of the threading alignments. Alignment with a Normalized Z-score >1 mean a good alignment and vice versa. (c) Download Templates provides the 3D structure of the aligned regions of the threading templates.

Reference:

J Zhang, J Yang, R Jang, Y Zhang, Novel hybrid approach to G protein-coupled receptor structure modeling and case study on human genome, submitted, 2014.

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