GPCR - GPCR-SSFE 2.0


A Homology Modeling Resource for G-Protein Coupled Receptors

Facts & Questions

What are the technical requirements for using SSFE?

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What is the purpose of the SSFE database?

SSFE is the first comprehensive, GPCR-focused database to store homology models that are based on the crystallographic advances made in the past few years. The fragment-based models stored in SSFE serve as a valuable starting-point for molecular analyses of GPCRs based on their structure, such as structure-based drug design or the detailed molecular analysis of mutations.


Which templates are used in the analysis?

We use all 27 inactive Class A GPCRs that were available at the time of doing the analysis:


Protein name Gene name Species Unique identifier Structure
RhodopsinRhobovinebRho1U19
Beta-2 adrenergic receptorB2ARhumanhB2AR2RH1
RhodopsinRhosquidsRho2Z73
Beta-1 adrenergic receptorB1arturkeytB1ar2VT4
Dopamin 3 receptorDRD3humanhDRD33PBL
Chemokine receptor type 4CXCR4humanhCXCR43ODU
Histamine H1 receptorHRH1humanhHRH13RZE
Sphingosine 1-phosphate receptor 1S1PR1humanhS1PR13V2Y
Muscarinic acetylcholine receptor M2CHRM2humanhCHRM23UON
Muscarinic acetylcholine receptor M3Chrm3ratrChrm34U15
Proteinase-activated receptor 1F2RhumanhF2R3VW7
Kappa-type opioid receptorOPRK1humanhOPRK14DJH
Mu-type opioid receptorOprm1mousemOprm14DKL
Nociceptin receptorOPRL1humanhOPRL14EA3
Delta-type opioid receptorOPRD1humanhOPRD14N6H
Adenosine receptor A2aADORA2AhumanhADORA2A4EIY
C-C chemokine receptor type 5CCR5humanhCCR54MBS
P2Y purinoceptor 12P2Y12humanhP2Y124NTJ
Delta-type opioid receptorOprd1mousemOprd14EJ4
Free fatty acid receptor 1FFAR1humanhFFAR14PHU
Angiotensin II type 1 receptorAGTR1humanhAGTR14YAY
Orexin receptor type 2HCRTR2humanhHCRTR24S0V
P2Y purinoceptor 1P2RY1humanhP2RY14XNV
Lysophosphatidic acid receptor 1LPAR1humanhLPAR14Z34
Orexin receptor type 1HCRTR1humanhHCRTR14ZJ8
Muscarinic acetylcholine receptor M1CHRM1humanhCHRM15CXV
Muscarinic acetylcholine receptor M4CHRM4humanhCHRM45DSG

How were the 1002 GPCR sequences aligned to the templates?

A multiple sequence alignment of the 27 available templates plus 50 other Class A GPCRs was generated. GPCRs were selected so as to maximise the coverage of the phylogenetic tree for Class A GPCRs. Using this alignment a HMMER profile was created. The hmmalign function was used to align query sequences against our GPCR profile.

The BioJS MSA-Viewer is used to displays the multiple sequence alignment used to create the HMMER profile


How were the templates selected for homology modelling?

The templates were selected based on our published workflow: Worth CL, Kleinau G and Krause G (2009) Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models. PLoS One 4(9): e7011.


Which features are stored in the fingerprint database guiding template selection?

Helix Fingerprint Motifs Ballesteros-Weinstein Region
TMH1CC1.43-1.44
TMH1EN1.49-1.50
TMH1PXXGGN1.45-1.50
TMH1P1.36
TMH1NG1.50-1.51
TMH1NS1.50-1.51
TMH1GXPXNF1.46-1.51
TMH1GXXGN1.46-1.50
TMH1FXXG1.43-1.46
TMH1GXXG1.40-1.43
TMH1GXXG1.43-1.46
TMH1CXXG1.43-1.46
TMH1Helix1 extension1.28-1.30
TMH1Helix1 extension1.24-1.30
TMH1Helix1 extension1.61-1.64
TMH1GXP1.46-1.48
TMH1GXPXNV1.46-1.51
TMH1GA1.56-1.57
TMH1G1.38
TMH1MXA1.47-1.49
TMH1AA1.37-1.38
TMH1TG1.39-1.40
TMH2P2.58
TMH2P2.59
TMH2TTT2.59-2.61
TMH2GG2.56-2.57
TMH2DXXXG2.50-2.54
TMH2N2.58
TMH2N2.59
TMH2DXAXG2.50-2.54
TMH2DXXF2.50-2.53
TMH2DXXA2.50-2.53
TMH2TXP2.56-2.58
TMH2TXP2.57-2.59
TMH2DXXX[small]2.50-2.54
TMH2Helix2 extension2.66-2.68
TMH2GC2.47-2.48
TMH2A2.43
TMH2SXP2.56-2.58
TMH2TXXP2.56-2.59
TMH2P2.38
TMH2PXS2.59-2.61
TMH3no_C3.25
TMH3GXXGGXXG3.29-3.36
TMH3CXXXXAA[aromatic][aromatic]3.25-3.33
TMH3RPXCXX[aromatic]3.22-3.28
TMH3CXXE3.25-3.28
TMH3GC3.24-3.25
TMH3CXXV3.25-3.28
TMH3GCXG3.24-3.27
TMH3P3.26
TMH3P3.35
TMH3GGG3.39-3.41
TMH3[tiny]RY3.49-3.51
TMH3DRWY3.49-3.52
TMH3P3.29
TMH3HRY3.49-3.51
TMH3G3.38
TMH3G3.30
TMH4P4.59
TMH4P4.60
TMH4no_P4.59
TMH4no_P4.60
TMH4GG4.57-4.58
TMH4G4.57
TMH4PP4.59-4.60
TMH4FF4.61-4.62
TMH4G4.56
TMH4PXP4.59-4.61
TMH4[aromatic]4.56
TMH4GXP4.57-4.59
TMH4[aromatic]XP4.57-4.59
TMH4[aromatic]XP4.58-4.60
TMH4GXWXP4.48-4.52
TMH4Helix4 extension4.34-4.38
TMH4G4.58
TMH4G4.62
TMH4G4.54
TMH4SXP4.57-4.59
TMH4SP4.58-4.59
TMH4E4.42
TMH4P4.39
TMH5no_P5.50
TMH5GXXGP5.46-5.50
TMH5PG5.50-5.51
TMH5G5.45
TMH5G5.46
TMH5no_F5.47
TMH5CV5.46-5.47
TMH5FFF5.46-5.48
TMH5HF5.46-5.47
TMH5GXXXAAF5.41-5.47
TMH5G5.42
TMH5G5.36
TMH5A5.46
TMH5CYXLM5.57-5.61
TMH5Helix5 extension5.65-5.68
TMH5Helix5 extension5.65-5.69
TMH5Helix5 extension5.65-5.72
TMH5Helix5 extension5.65-5.77
TMH5Helix5 extension5.30-5.35
TMH5GP5.36-5.37
TMH5SXXXP5.46-5.50
TMH5G5.37
TMH5PF5.50-5.51
TMH5T5.46
TMH5GXXG5.56-5.58
TMH5N5.47
TMH5PXT5.50-5.52
TMH6GP6.49-6.50
TMH6no_FXXCWXP6.44-6.50
TMH6GXXXG6.38-6.42
TMH6FTXCWXP6.44-6.50
TMH6FXXSWXP6.44-6.50
TMH6N6.52
TMH6LLLL6.54-6.57
TMH6FXXMWXP6.44-6.50
TMH6Q6.36
TMH6G6.53
TMH6G6.54
TMH6H6.32
TMH6PFF6.50-6.52
TMH6G6.42
TMH6no_G6.38
TMH6Helix6 extension6.27-6.30
TMH6Helix6 extension6.21-6.30
TMH6Helix6 extension6.61-6.64
TMH6GG6.38-6.39
TMH6no_[aromatic]6.48
TMH6H6.51
TMH6PXS6.50-6.52
TMH6SYXP6.47-6.50
TMH6SP6.49-6.50
TMH6TP6.49-6.50
TMH6G6.51
TMH7DPXXY7.49-7.53
TMH7CC7.46-7.47
TMH7S7.45
TMH7YXSSA7.43-7.47
TMH7P7.31
TMH7P7.38
TMH7P7.32
TMH7PXM7.38-7.40
TMH7CXALGY7.38-7.43
TMH7VXXVXNSG7.40-7.47
TMH7Helix7 extension7.28-7.31
TMH7Helix7 extension7.24-7.31
TMH7no_Y7.53
TMH7G7.54
TMH7P7.36-7.38
TMH7PXT7.36-7.38
TMH7CXA7.40-7.42
TMH7GYWXCY7.38-7.43
TMH7G7.40
TMH7CXDP7.47-7.50
TMH7A7.51
TMH7G7.57


How are the homology models produced?

The homology models are produced using Modeller (9.14). Three models are produced and the model with the best DOPE score is made available for download by the user.


How do I format a sequence file in FASTA format?

The first line in a FASTA file starts with a ">" and is used for a unique description of the sequence. Afterwards follows the actual sequence itself in standard one-letter code. A sample file in FASTA format can be viewed here.


How do search GPCR-SSFE 2.0 for pre-calculated models?

If the quality of the video is not good, please click on the cog icon at the bottom of the you tube player and select a higher resolution.


How do I submit a modeling job to GPCR-SSFE 2.0?

If the quality of the video is not good, please click on the cog icon at the bottom of the you tube player and select a higher resolution.


How do interpret the results returned by GPCR-SSFE 2.0?

If the quality of the video is not good, please click on the cog icon at the bottom of the you tube player and select a higher resolution.


Why does SSFE take so long to return the results?

Results should be returned within 5 minutes. It takes several minutes for us to validate that a query sequence is suitable for analysis by SSFE and then several more minutes for Modeller to produce the homology models.


How do I interpret the Ramachandran plot analysis?

The best known way to check the stereochemical quality of a protein structure is by calculating a Ramachandran plot. This is a plot of the phi main chain torsion angle verses the psi main chain torsion angle of every amino acid residue in a protein. In the resulting scatterplot, the points tend to cluster in particular favourable regions and tend not to fall within the disallowed regions. These disallowed regions are where steric hindrance between side chain atoms make certain phi psi combinations difficult or even impossible to occur. Therefore, when assessing the Ramanchandran plot for your GPCR of interest, it is the residues in disallowed regions that give an indication of the model quality. For more information please see the Ramanchandran plots analysis page provided by Procheck.


How do I interpret the loop modeling results?

The structure is shown in grey and the loops are displayed in different colours. Below the embedded viewer, where calculated, the single loops can be selected. By default, the best result is selected and shown. Additionally, sidechains (not minimized) and labels can be displayed, the structure can spin, the background colour can be changed and the currently displayed structure can be downloaded. The structure within the NGL viewer can be centred by a click of the mouse weel on the structure.

The results table provides information about each calculated loop. "Run" indicates whether the stem residues have been increased at N- and C-termini by 0-3 residues. If the loop stems have been changed, the sequence shown increases accordingly. Only results with a sequence length smaller than 35 residues and less than 5 clashes have been selected. The results are sorted by their score. If the score of two results differ less than 30%, the loop with less clashes is ranked higher. Where a crystal structure of a GPCR is used to model a loop, the score has been doubled, to rank this loop more highly. The information about the templates include their sequence, PDB-id and position within the structure.


How should I cite SSFE?

GPCR-SSFE 2.0 is detailed in the following paper:
Worth CL, Kreuchwig F, Tiemann JKS, Kreuchwig A, Ritschel M, Kleinau G, Hildebrand PW and Krause G (2017) GPCR-SSFE 2.0—a fragment-based molecular modeling web tool for Class A G-protein coupled receptors . Nucleic Acids Res.