GPCR Sequence:

>tr|B2R7P1|B2R7P1_HUMAN cDNA, FLJ93535, Homo sapiens opioid receptor, kappa 1 (OPRK1), mRNA OS=Homo sapiens PE=2 SV=1
MESPIQIFRGEPGPTCAPSACLPPNSSAWFPGWAEPDSNGSAGSEDAQLEPAHISPAIPV
IITAVYSVVFVVGLVGNSLVMFVIIRYTKMKTATNIYIFNLALADALVTTTMPFQSTVYL
MNSWPFGDVLCKIVISIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRTPLKAKIINI
CIWLLSSSVGISAIVLGGTKVREDVDVIECSLQFPDDDYSWWDLFMKICVFIFAFVIPVL
IIIVCYTLMILRLKSVRLLSGSREKDRNLRRITRLVLVVVAVFVVCWTPIHIFILVEALG
STSHSTAALSSYYFCIALGYTNSSLNPILYAFLDENFKRCFRDFCFPLKMRMERQSTSRV
RNTVQDPAYLRDIDGMNKPV

Estimation of the GPCR-I-TASSER model for B2R7P1

C-score = -0.280
TM-score = 0.680 (estimated)
RMSD = 7.3 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	2ks9A	3.010	template1
2	2rh1_A	6.248	template2
3	2ks9a	3.246	template3
4	2ks9a	6.191	template4
5	1l9ha	4.163	template5
6	2ks9A	5.347	template6
7	2rh1_A	5.498	template7
8	hs1u19	3.119	template8
9	2ks9a	5.943	template9
10	3pblA1	2.403	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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