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GPCR-SSFE: a comprehensive database of G-protein-coupled receptor template predictions and homology models.

Worth CL, Kreuchwig A, Kleinau G, Krause G - BMC Bioinformatics (2011)

Bottom Line: However, many researchers working on GPCRs are not experienced homology modellers and are therefore unable to benefit from the information that can be gleaned from such three-dimensional models.The data provided by GPCR-SSFE are useful for investigating general and detailed sequence-structure-function relationships of GPCRs, performing structure-based drug design and for better understanding the molecular mechanisms underlying disease-associated mutations in GPCRs.The effectiveness of our multiple template and fragment approach is demonstrated by the accuracy of our predicted homology models compared to recently published crystal structures.

View Article: PubMed Central - HTML - PubMed

Affiliation: Leibniz-Institut für Molekulare Pharmakologie, 13125 Berlin, Germany.

ABSTRACT

Background: G protein-coupled receptors (GPCRs) transduce a wide variety of extracellular signals to within the cell and therefore have a key role in regulating cell activity and physiological function. GPCR malfunction is responsible for a wide range of diseases including cancer, diabetes and hyperthyroidism and a large proportion of drugs on the market target these receptors. The three dimensional structure of GPCRs is important for elucidating the molecular mechanisms underlying these diseases and for performing structure-based drug design. Although structural data are restricted to only a handful of GPCRs, homology models can be used as a proxy for those receptors not having crystal structures. However, many researchers working on GPCRs are not experienced homology modellers and are therefore unable to benefit from the information that can be gleaned from such three-dimensional models. Here, we present a comprehensive database called the GPCR-SSFE, which provides initial homology models of the transmembrane helices for a large variety of family A GPCRs.

Description: Extending on our previous theoretical work, we have developed an automated pipeline for GPCR homology modelling and applied it to a large set of family A GPCR sequences. Our pipeline is a fragment-based approach that exploits available family A crystal structures. The GPCR-SSFE database stores the template predictions, sequence alignments, identified sequence and structure motifs and homology models for 5025 family A GPCRs. Users are able to browse the GPCR dataset according to their pharmacological classification or search for results using a UniProt entry name. It is also possible for a user to submit a GPCR sequence that is not contained in the database for analysis and homology model building. The models can be viewed using a Jmol applet and are also available for download along with the alignments.

Conclusions: The data provided by GPCR-SSFE are useful for investigating general and detailed sequence-structure-function relationships of GPCRs, performing structure-based drug design and for better understanding the molecular mechanisms underlying disease-associated mutations in GPCRs. The effectiveness of our multiple template and fragment approach is demonstrated by the accuracy of our predicted homology models compared to recently published crystal structures.

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The home page of the GPCR-SSFE database. The menu at the top of the page allows users to easily navigate the site. The background to the database is provided, along with information about the templates used for homology modelling.
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Figure 1: The home page of the GPCR-SSFE database. The menu at the top of the page allows users to easily navigate the site. The background to the database is provided, along with information about the templates used for homology modelling.

Mentions: The GPCR-SSFE has a user-friendly interface with a menu and a facts and questions (FAQ) page to aid usability. On the homepage of GPCR-SSFE (Figure 1), users can find information about the database and the template structures used for analysis and homology modelling, including a link to a Jmol applet showing the five template structures superimposed onto one another (Figure 2).


GPCR-SSFE: a comprehensive database of G-protein-coupled receptor template predictions and homology models.

Worth CL, Kreuchwig A, Kleinau G, Krause G - BMC Bioinformatics (2011)

The home page of the GPCR-SSFE database. The menu at the top of the page allows users to easily navigate the site. The background to the database is provided, along with information about the templates used for homology modelling.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3113946&req=5

Figure 1: The home page of the GPCR-SSFE database. The menu at the top of the page allows users to easily navigate the site. The background to the database is provided, along with information about the templates used for homology modelling.
Mentions: The GPCR-SSFE has a user-friendly interface with a menu and a facts and questions (FAQ) page to aid usability. On the homepage of GPCR-SSFE (Figure 1), users can find information about the database and the template structures used for analysis and homology modelling, including a link to a Jmol applet showing the five template structures superimposed onto one another (Figure 2).

Bottom Line: However, many researchers working on GPCRs are not experienced homology modellers and are therefore unable to benefit from the information that can be gleaned from such three-dimensional models.The data provided by GPCR-SSFE are useful for investigating general and detailed sequence-structure-function relationships of GPCRs, performing structure-based drug design and for better understanding the molecular mechanisms underlying disease-associated mutations in GPCRs.The effectiveness of our multiple template and fragment approach is demonstrated by the accuracy of our predicted homology models compared to recently published crystal structures.

View Article: PubMed Central - HTML - PubMed

Affiliation: Leibniz-Institut für Molekulare Pharmakologie, 13125 Berlin, Germany.

ABSTRACT

Background: G protein-coupled receptors (GPCRs) transduce a wide variety of extracellular signals to within the cell and therefore have a key role in regulating cell activity and physiological function. GPCR malfunction is responsible for a wide range of diseases including cancer, diabetes and hyperthyroidism and a large proportion of drugs on the market target these receptors. The three dimensional structure of GPCRs is important for elucidating the molecular mechanisms underlying these diseases and for performing structure-based drug design. Although structural data are restricted to only a handful of GPCRs, homology models can be used as a proxy for those receptors not having crystal structures. However, many researchers working on GPCRs are not experienced homology modellers and are therefore unable to benefit from the information that can be gleaned from such three-dimensional models. Here, we present a comprehensive database called the GPCR-SSFE, which provides initial homology models of the transmembrane helices for a large variety of family A GPCRs.

Description: Extending on our previous theoretical work, we have developed an automated pipeline for GPCR homology modelling and applied it to a large set of family A GPCR sequences. Our pipeline is a fragment-based approach that exploits available family A crystal structures. The GPCR-SSFE database stores the template predictions, sequence alignments, identified sequence and structure motifs and homology models for 5025 family A GPCRs. Users are able to browse the GPCR dataset according to their pharmacological classification or search for results using a UniProt entry name. It is also possible for a user to submit a GPCR sequence that is not contained in the database for analysis and homology model building. The models can be viewed using a Jmol applet and are also available for download along with the alignments.

Conclusions: The data provided by GPCR-SSFE are useful for investigating general and detailed sequence-structure-function relationships of GPCRs, performing structure-based drug design and for better understanding the molecular mechanisms underlying disease-associated mutations in GPCRs. The effectiveness of our multiple template and fragment approach is demonstrated by the accuracy of our predicted homology models compared to recently published crystal structures.

Show MeSH
Related in: MedlinePlus