ArticlePloS one2013
Towards improved quality of GPCR models by usage of multiple templates and profile-profile comparison.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 54 citations in OpenAlex.
- GPCRVS - AI-driven Decision Support System for GPCR Virtual Screening.International journal of molecular sciences · 2025Article
- Helix 8 in chemotactic receptors of the complement system.PLoS computational biology · 2022Article
- Signal Transduction by VIP and PACAP Receptors.Biomedicines · 2022Review
- The Many Faces of G Protein-Coupled Receptor 143, an Atypical Intracellular Receptor.Frontiers in molecular biosciences · 2022Review
- Class A and C GPCR Dimers in Neurodegenerative Diseases.Current neuropharmacology · 2022Review
- Drug Repositioning For Allosteric Modulation of VIP and PACAP Receptors.Frontiers in endocrinology · 2021Article
- A Molecular Dynamics Study of Vasoactive Intestinal Peptide Receptor 1 and the Basis of Its Therapeutic Antagonism.International journal of molecular sciences · 2019Article
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- Comparative Modeling and Evaluation of Leukotriene B4 Receptors for Selective Drug Discovery Towards the Treatment of Inflammatory Diseases.The protein journal · 2018Article
- GPCRM: a homology modeling web service with triple membrane-fitted quality assessment of GPCR models.Nucleic acids research · 2018Article
- Rosetta Broker for membrane protein structure prediction: concentrative nucleoside transporter 3 and corticotropin-releasing factor receptor 1 test cases.BMC structural biology · 2017Article
- Identifying ligands at orphan GPCRs: current status using structure-based approaches.British journal of pharmacology · 2016Review
- GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors.Nucleic acids research · 2016Article
- GPCRdb: the G protein-coupled receptor database - an introduction.British journal of pharmacology · 2016Review
- Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications.PLoS computational biology · 2016Article
- GPCRdb: an information system for G protein-coupled receptors.Nucleic acids research · 2016Article
- What can we learn from molecular dynamics simulations for GPCR drug design?Computational and structural biotechnology journal · 2015Article
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Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledG-protein coupled receptors (GPCRs) are targets of nearly one third of the drugs at the current pharmaceutical market. Despite their importance in many cellular processes the crystal structures are available for less than 20 unique GPCRs of the Rhodopsin-like class. Fortunately, even though involved in different signaling cascades, this large group of membrane proteins has preserved a uniform structure comprising seven transmembrane helices that allows quite reliable comparative modeling. Nevertheless, low sequence similarity between the GPCR family members is still a serious obstacle not only in template selection but also in providing theoretical models of acceptable quality. An additional level of difficulty is the prediction of kinks and bulges in transmembrane helices. Usage of multiple templates and generation of alignments based on sequence profiles may increase the rate of success in difficult cases of comparative modeling in which the sequence similarity between GPCRs is exceptionally low. Here, we present GPCRM, a novel method for fast and accurate generation of GPCR models using averaging of multiple template structures and profile-profile comparison. In particular, GPCRM is the first GPCR structure predictor incorporating two distinct loop modeling techniques: Modeller and Rosetta together with the filtering of models based on the Z-coordinate. We tested our approach on all unique GPCR structures determined to date and report its performance in comparison with other computational methods targeting the Rhodopsin-like class. We also provide a database of precomputed GPCR models of the human receptors from that class. AVAILABILITY: GPCRM SERVER AND DATABASE: http://gpcrm.biomodellab.eu.
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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.