GPCR Sequence:

>tr|Q5T6D8|Q5T6D8_HUMAN Neuropeptide FF receptor 1 (Fragment) OS=Homo sapiens GN=NPFFR1 PE=2 SV=1
GEPSQPPNSSWPLSQNGTNTEATPATNLTFSSYYQHTSPVAAMFIVAYALIFLLCMVGNT
LVCFIVLKNRHMHTVTNMFILNLAVSDLLVGIFCMPTTLVDNLITGWPFDNATCKMSGLV
QGMSVSASVFTLVAIAVERFRCIVHPFREKLTLRKALVTIAVIWALALLIMCPSAVTLTV
TREEHHFMVDARNRSYPLYSCWEAWPEKGMRRVYTTVLFSHIYLAPLALIVVMYARIARK
LCQAPGPAPGGEEAADPRASRRRARVVHMLVMVALFFTLSWLPLWALLLLIDYGQLSAPQ
LHLVTVYAFPFAHWLAFFNSSANPIIYGYFNENFRRGFQAAFRARLCPRPSGSHKEAYSE
RPGGLLHRRVFVVVRPSDSGLPSESGPSSGAPRPGRLPLRNGRVAHHGLPREGPGCSHLP
LTIPAWDI

Estimation of the GPCR-I-TASSER model for Q5T6D8

C-score = -0.600
TM-score = 0.640 (estimated)
RMSD = 8.3 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	3.004	template1
2	2rh1_A	6.264	template2
3	2ks9a	2.722	template3
4	2ks9a	6.249	template4
5	2ks9A	4.013	template5
6	2ks9A	4.650	template6
7	2rh1_A	5.394	template7
8	hs1f88	3.014	template8
9	2ks9a	6.112	template9
10	2ks9A1	2.344	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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