SI Table 3 Results of scoring according to all-atom energy values. The RMSD values between backbone atoms of three extracellular loops and their native counterparts are presented.

GPCR (ref. structure)	RMSDBEST Å	RMSDLE Å	RMSDLE10 Å	RMSDLE100 Å
A2AR	4.67	5.88	5.88	5.88
ADRB1	3.28	5.81	3.57	3.40
ADRB2	3.38	5.51	4.43	3.82
CHRM2	2.65	5.12	2.87	2.87
CHRM3	2.53	4.65	4.11	2.98
CXCR4	2.41	3.08	3.08	2.41
DRD3	2.14	3.43	2.88	2.36
NTSR1	2.99	8.82	4.74	3.70
OPRD1	1.92	5.04	3.63	2.93
OPRM1	1.92	6.78	3.22	2.43
OPRL1	4.47	6.22	5.48	4.55
RHO	4.20	8.21	4.68	4.31
S1PR1	4.40	7.40	7.40	6.86

RMSD^BEST – the lowest RMSD observed in all CABS generated models
RMSD^LE – the RMSD value for the loop corresponding to the model with the lowest potential energy
RMSD^LE10 – the lowest RMSD value for ECL2 observed among 10 models presenting the lowest potential energy
RMSD^LE100 – the lowest RMSD values for ECL2 observed among 100 models presenting the lowest potential energy

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SI Table 4 Results of scoring according to structural clustering. The RMSD values between backbone atoms of three extracellular loops and their native counterparts are presented.

GPCR (ref. structure)	RMSDBEST Å	RMSDLC Å	RMSDLC10 Å	RMSDLC100 Å
A2AR	4.67	8.74	5.00	5.85
ADRB1	3.28	6.85	5.33	3.28
ADRB2	3.38	6.73	4.41	3.38
CHRM2	2.65	4.13	3.70	2.65
CHRM3	2.53	4.64	3.89	2.63
CXCR4	2.41	3.56	3.56	3.56
DRD3	2.14	6.10	2.57	2.36
NTSR1	2.99	7.84	4.82	3.70
OPRD1	1.92	4.88	3.24	2.08
OPRM1	1.92	6.96	2.24	1.92
OPRL1	4.47	9.33	5.80	5.56
RHO	4.20	5.11	5.11	4.36
S1PR1	4.40	8.49	7.66	5.85

RMSD^BEST – the lowest RMSD observed in all CABS generated models
RMSD^LC – the RMSD value for the loop corresponding to the representative model of the largest cluster from CABS simulations
RMSD^LC10 – the lowest RMSD values for ECL2 observed among 10 models representing the 10 largest clusters
RMSD^LC100 – the lowest RMSD values for ECL2 observed among 100 models representing the 100 largest clusters

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GPCR modeling decoys set All-atom models from CABS pseudotrajectory (4000 models per protein)

GPCR	decoys set multimodel pdb	decoys set one model per file
A2AR	multimodel PDB	one model per file
ADRB1	multimodel PDB	one model per file
ADRB2	multimodel PDB	one model per file
CHRM2	multimodel PDB	one model per file
CHRM3	multimodel PDB	one model per file
CXCR4	multimodel PDB	one model per file
DRD3	multimodel PDB	one model per file
NTSR1	multimodel PDB	one model per file
OPRD1	multimodel PDB	one model per file
OPRL1	multimodel PDB	one model per file
OPRM1	multimodel PDB	one model per file
RHO	multimodel PDB	one model per file
S1PR1	multimodel PDB	one model per file

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Download script for calculating loop RMSD after whole structure superimposition (require CSB)

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Last modified: Tue Jun 3 20:31:28 CEST 2014