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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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Related in: MedlinePlus

GPCR-SSFE sequence submission page. Where a family A GPCR is not contained in the database, a user may submit their sequence of interest to GPCR-SSFE for template prediction and homology modelling. Users must obtain a licence key for Modeller before they are able to use this function.
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Figure 5: GPCR-SSFE sequence submission page. Where a family A GPCR is not contained in the database, a user may submit their sequence of interest to GPCR-SSFE for template prediction and homology modelling. Users must obtain a licence key for Modeller before they are able to use this function.

Mentions: In some instances, GPCR-SSFE might not store results for particular family A GPCRs e.g. newly identified orphan GPCRs. For such cases, users can submit their GPCR sequence (in FASTA format) to GPCR-SSFE for analysis and homology model building by navigating to the "Run SSFE" webpage (Figure 5). Modeller 9v7 is used for homology modelling, therefore, users must obtain a Modeller license key before they can use this tool. This key is freely available for academic users and easily obtainable at: http://salilab.org/modeller/registration.shtml. To start the template analysis and homology modelling, the user enters their GPCR sequence onto the webpage (by either uploading or copying and pasting it), along with their Modeller licence key and email address. Once the results are ready, a web-link is emailed to the user. Results are stored on the server for seven days. The results page looks exactly like those retrieved when searching the database, except that links to external databases are not provided.


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)

GPCR-SSFE sequence submission page. Where a family A GPCR is not contained in the database, a user may submit their sequence of interest to GPCR-SSFE for template prediction and homology modelling. Users must obtain a licence key for Modeller before they are able to use this function.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: GPCR-SSFE sequence submission page. Where a family A GPCR is not contained in the database, a user may submit their sequence of interest to GPCR-SSFE for template prediction and homology modelling. Users must obtain a licence key for Modeller before they are able to use this function.
Mentions: In some instances, GPCR-SSFE might not store results for particular family A GPCRs e.g. newly identified orphan GPCRs. For such cases, users can submit their GPCR sequence (in FASTA format) to GPCR-SSFE for analysis and homology model building by navigating to the "Run SSFE" webpage (Figure 5). Modeller 9v7 is used for homology modelling, therefore, users must obtain a Modeller license key before they can use this tool. This key is freely available for academic users and easily obtainable at: http://salilab.org/modeller/registration.shtml. To start the template analysis and homology modelling, the user enters their GPCR sequence onto the webpage (by either uploading or copying and pasting it), along with their Modeller licence key and email address. Once the results are ready, a web-link is emailed to the user. Results are stored on the server for seven days. The results page looks exactly like those retrieved when searching the database, except that links to external databases are not provided.

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