1
|
Worth CL, Kreuchwig F, Tiemann JKS, Kreuchwig A, Ritschel M, Kleinau G, Hildebrand PW, Krause G. GPCR-SSFE 2.0-a fragment-based molecular modeling web tool for Class A G-protein coupled receptors. Nucleic Acids Res 2019; 45:W408-W415. [PMID: 28582569 PMCID: PMC5570183 DOI: 10.1093/nar/gkx399] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/03/2017] [Indexed: 11/14/2022] Open
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.
Collapse
Affiliation(s)
- Catherine L Worth
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), D-13125 Berlin, Germany
| | - Franziska Kreuchwig
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), D-13125 Berlin, Germany
| | - Johanna K S Tiemann
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, D-10117 Berlin, Germany
| | - Annika Kreuchwig
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), D-13125 Berlin, Germany
| | - Michele Ritschel
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, D-10117 Berlin, Germany
| | - Gunnar Kleinau
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, D-10117 Berlin, Germany.,Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin, D-13353 Berlin, Germany
| | - Peter W Hildebrand
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, D-10117 Berlin, Germany.,Institute of Medical Physics and Biophysics, Leipzig University, D-04107 Leipzig, Germany
| | - Gerd Krause
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), D-13125 Berlin, Germany
| |
Collapse
|