ArticleBiophysical journal2014
Structure prediction of the second extracellular loop in G-protein-coupled receptors.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 38 citations in OpenAlex.
- CABS-flex 3.0: an online tool for simulating protein structural flexibility and peptide modeling.Nucleic acids research · 2025Article
- Integrative modeling of diverse protein-peptide systems using CABS-dock.PLoS computational biology · 2023Article
- Multiscale Modeling of Amyloid Fibrils Formed by Aggregating Peptides Derived from the Amyloidogenic Fragment of the A-Chain of Insulin.International journal of molecular sciences · 2021Article
- Flexible docking of peptides to proteins using CABS-dock.Protein science : a publication of the Protein Society · 2020Article
- Antimicrobial Peptide Designing and Optimization Employing Large-Scale Flexibility Analysis of Protein-Peptide Fragments.ACS omega · 2019Article
- Molecular insights into the interaction of hemorphin and its targets.Scientific reports · 2019Article
- Phage antibody library screening for the selection of novel high-affinity human single-chain variable fragment against gastrin receptor: an in silico and in vitro study.Daru : journal of Faculty of Pharmacy, Tehran University of Medical Sciences · 2019Article
- A benchmark study of loop modeling methods applied to G protein-coupled receptors.Journal of computer-aided molecular design · 2019Article
- Identification of avian vasotocin receptor subtype-specific antagonists involved in the stress response of the chicken, Gallus gallus.Journal of biomolecular structure & dynamics · 2019Article
- Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields.International journal of molecular sciences · 2019Review
- Using Dimensionality Reduction to Analyze Protein Trajectories.Frontiers in molecular biosciences · 2019Article
- Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models.International journal of molecular sciences · 2018Review
- Optical Control of Dopamine Receptors Using a Photoswitchable Tethered Inverse Agonist.Journal of the American Chemical Society · 2017Article
- A protocol for CABS-dock protein-peptide docking driven by side-chain contact information.Biomedical engineering online · 2017Article
- Modeling EphB4-EphrinB2 protein-protein interaction using flexible docking of a short linear motif.Biomedical engineering online · 2017Article
- Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction.Scientific reports · 2016Article
- CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site.Nucleic acids research · 2015Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
G-protein-coupled receptors (GPCRs) play key roles in living organisms. Therefore, it is important to determine their functional structures. The second extracellular loop (ECL2) is a functionally important region of GPCRs, which poses significant challenge for computational structure prediction methods. In this work, we evaluated CABS, a well-established protein modeling tool for predicting ECL2 structure in 13 GPCRs. The ECL2s (with between 13 and 34 residues) are predicted in an environment of other extracellular loops being fully flexible and the transmembrane domain fixed in its x-ray conformation. The modeling procedure used theoretical predictions of ECL2 secondary structure and experimental constraints on disulfide bridges. Our approach yielded ensembles of low-energy conformers and the most populated conformers that contained models close to the available x-ray structures. The level of similarity between the predicted models and x-ray structures is comparable to that of other state-of-the-art computational methods. Our results extend other studies by including newly crystallized GPCRs.
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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.