GPCR-SSFE 2.0—a fragment-based molecular modeling web tool for Class A G-protein coupled receptors

By Catherine L. Worth, Franziska Kreuchwig, Johanna K. S. Tiemann, Annika Kreuchwig, Michele Ritschel, Gunnar Kleinau, Peter Werner Hildebrand, Gerd Krause. 2017

30 citations recorded by the source corpus.

Abstract G-protein coupled receptors (GPCRs) are key players in signal transduction and therefore a large proportion of pharmaceutical drugs target these receptors. Structural data of GPCRs are sparse yet important for elucidating the molecular basis of GPCR-related diseases and for performing structure-based drug design. To ameliorate this problem, GPCR-SSFE 2.0 (http://www.ssfa-7tmr.de/ssfe2/), an intuitive web server dedicated to providing three-dimensional Class A GPCR homology models has been developed. The updated web server includes 27 inactive template structures and incorporates various new functionalities. Uniquely, it uses a fingerprint correlation scoring strategy for identifying the optimal templates, which we demonstrate captures structural features that sequence similarity alone is unable to do. Template selection is carried out separately for each helix, allowing both single-template models and fragment-based models to be built. Additionally, GPCR-SSFE 2.0 stores a comprehensive set of pre-calculated and downloadable homology models and also incorporates interactive loop modeling using the tool SL2, allowing knowledge-based input by the user to guide the selection process. For visual analysis, the NGL viewer is embedded into the result pages. Finally, blind-testing using two recently published structures shows that GPCR-SSFE 2.0 performs comparably or better than other state-of-the art GPCR modeling web servers.

Subfields: Cellular and Molecular Neuroscience, Molecular Biology

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Citations in the corpus

Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs (2020, methodology): “Of note, the GPCR-SSFE database lacked a structure of the D2 receptor for comparison.”
GPCRM: a homology modeling web service with triple membrane-fitted quality assessment of GPCR models (2018, background): “Currently, in GPCRM service there is no limitations on the number of templates used during model building which is especially needed when the required model should include fragments from several GPCR templates one by one, as it in GPCR-SSFE (16) or GPCRdb (1).”