GPCR Sequence:

>sp|P41586|PACR_HUMAN Pituitary adenylate cyclase-activating polypeptide type I receptor OS=Homo sapiens GN=ADCYAP1R1 PE=1 SV=1
MAGVVHVSLAALLLLPMAPAMHSDCIFKKEQAMCLEKIQRANELMGFNDSSPGCPGMWDN
ITCWKPAHVGEMVLVSCPELFRIFNPDQVWETETIGESDFGDSNSLDLSDMGVVSRNCTE
DGWSEPFPHYFDACGFDEYESETGDQDYYYLSVKALYTVGYSTSLVTLTTAMVILCRFRK
LHCTRNFIHMNLFVSFMLRAISVFIKDWILYAEQDSNHCFISTVECKAVMVFFHYCVVSN
YFWLFIEGLYLFTLLVETFFPERRYFYWYTIIGWGTPTVCVTVWATLRLYFDDTGCWDMN
DSTALWWVIKGPVVGSIMVNFVLFIGIIVILVQKLQSPDMGGNESSIYLRLARSTLLLIP
LFGIHYTVFAFSPENVSKRERLVFELGLGSFQGFVVAVLYCFLNGEVQAEIKRKWRSWKV
NRYFAVDFKHRHPSLASSGVNGGTQLSILSKSSSQIRMSGLPADNLAT

Estimation of the GPCR-I-TASSER model for P41586

C-score = -3.330
TM-score = 0.340 (estimated)
RMSD = 15.5 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	1.347	template1
2	2jod_A	5.322	template2
3	3a6pA1	1.497	template3
4	2joda	2.452	template4
5	2ks9A	1.474	template5
6	2jod_A	5.106	template6
7	2ziya	1.191	template7
8	hs2jod	2.937	template8
9	1i1ip	1.484	template9
10	2joda	2.075	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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