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

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Item Type:Article
Title:GPCR-SSFE 2.0: a fragment-based molecular modeling web tool for Class A G-protein coupled receptors
Creators Name:Worth, C.L. and Kreuchwig, F. and Tiemann, J.K.S. and Kreuchwig, A. and Ritschel, M. and Kleinau, G. and Hildebrand, P.W. and Krause, G.
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.
Keywords:Internet, G-Protein-Coupled Receptors, Molecular Models, Protein Sequence Analysis, Protein Structural Homology, Sequence Alignment, Software, Animals
Source:Nucleic Acids Research
Publisher:Oxford University Press
Page Range:W408-W415
Date:3 July 2017
Official Publication:https://doi.org/10.1093/nar/gkx399
PubMed:View item in PubMed

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