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.

How were the 5025 GPCR sequences aligned to the templates?

A multiple sequence alignment of the five available templates plus 54 other family A GPCRs was generated. GPCRs were selected so as to maximise the coverage of the phylogenetic tree for Family A GPCRs. Using this alignment a HMMER profile was created. The hmmalign function was used to align query sequences against our GPCR profile.

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.

How are the homology models produced?

The homology models are produced using Modeller (9v7). 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.

Why does SSFE take so long to return the results?

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 should I cite SSFE?

Worth CL, Kreuchwig A, Kleinau G, Krause G (2011) GPCR-SSFE: a comprehensive database of G-protein-coupled receptor template predictions and homology models. BMC Bioinformatics. 2011 May 23;12:185.