ArticleNucleic acids research2017
GPCR-SSFE 2.0-a fragment-based molecular modeling web tool for Class A G-protein coupled receptors.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 35 citations in OpenAlex.
- Elucidating the Structure and Activation Mechanisms of GPCRs Using Modern Computational and AI Tools.Cell biochemistry and biophysics · 2026Review
- Improving the Modeling of Extracellular Ligand Binding Pockets in RosettaGPCR for Conformational Selection.International journal of molecular sciences · 2023Article
- Combination of Docking-Based and Pharmacophore-Based Virtual Screening Identifies Novel Agonists That Target the Urotensin Receptor.Molecules (Basel, Switzerland) · 2022Article
- Evolutionary analyses reveal immune cell receptor GPR84 as a conserved receptor for bacteria-derived molecules.iScience · 2022Article
- Review
- Discovery and Characterization of Novel Antagonists of the Proinflammatory Orphan Receptor GPR84.ACS pharmacology & translational science · 2021Article
- BIO-GATS: A Tool for Automated GPCR Template Selection Through a Biophysical Approach for Homology Modeling.Frontiers in molecular biosciences · 2021Article
- Homology Modeling of Class A G-Protein-Coupled Receptors in the Age of the Structure Boom.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs.PLoS computational biology · 2020Article
- F2r negatively regulates osteoclastogenesis through inhibiting the Akt and NFκB signaling pathways.International journal of biological sciences · 2020Article
- Hybrid MM/CG Webserver: Automatic Set Up of Molecular Mechanics/Coarse-Grained Simulations for Human G Protein-Coupled Receptor/Ligand Complexes.Frontiers in molecular biosciences · 2020Article
- A Molecular Dynamics Study of Vasoactive Intestinal Peptide Receptor 1 and the Basis of Its Therapeutic Antagonism.International journal of molecular sciences · 2019Article
- Understanding Ligand Binding to G-Protein Coupled Receptors Using Multiscale Simulations.Frontiers in molecular biosciences · 2019Review
- GPCRM: a homology modeling web service with triple membrane-fitted quality assessment of GPCR models.Nucleic acids research · 2018Article
- Binding, Thermodynamics, and Selectivity of a Non-peptide Antagonist to the Melanocortin-4 Receptor.Frontiers in pharmacology · 2018Article
- Structural determinants of a conserved enantiomer-selective carvone binding pocket in the human odorant receptor OR1A1.Cellular and molecular life sciences : CMLS · 2017Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.