GPCR Sequence:

>sp|O95977|S1PR4_HUMAN Sphingosine 1-phosphate receptor 4 OS=Homo sapiens GN=S1PR4 PE=1 SV=1
MNATGTPVAPESCQQLAAGGHSRLIVLHYNHSGRLAGRGGPEDGGLGALRGLSVAASCLV
VLENLLVLAAITSHMRSRRWVYYCLVNITLSDLLTGAAYLANVLLSGARTFRLAPAQWFL
REGLLFTALAASTFSLLFTAGERFATMVRPVAESGATKTSRVYGFIGLCWLLAALLGMLP
LLGWNCLCAFDRCSSLLPLYSKRYILFCLVIFAGVLATIMGLYGAIFRLVQASGQKAPRP
AARRKARRLLKTVLMILLAFLVCWGPLFGLLLADVFGSNLWAQEYLRGMDWILALAVLNS
AVNPIIYSFRSREVCRAVLSFLCCGCLRLGMRGPGDCLARAVEAHSGASTTDSSLRPRDS
FRGSRSLSFRMREPLSSISSVRSI

Estimation of the GPCR-I-TASSER model for O95977

C-score = 0.080
TM-score = 0.720 (estimated)
RMSD = 6.6 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	2g87A	2.802	template1
2	2rh1_A	6.353	template2
3	1l9ha	3.651	template3
4	2z73a	6.646	template4
5	2ks9A	3.742	template5
6	2g87A	4.668	template6
7	1u19_A	6.136	template7
8	hs1u19	5.426	template8
9	2z73a	6.457	template9
10	2pedA	2.746	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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