ArticleBriefings in bioinformatics2021
Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement.
Article in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 17 citations in OpenAlex.
- DeorphaNN: Virtual screening of GPCR peptide agonists using AlphaFold-predicted active-state complexes and deep learning embeddings.Molecular cell · 2026Article
- Peptide-based drug design using generative AI.Chemical communications (Cambridge, England) · 2026Review
- Assessment of generative de novo peptide design methods for G protein-coupled receptors.PloS one · 2026Article
- Identification of a novel MIPEP splice variant with altered substrate-binding properties.Biochemistry and biophysics reports · 2025Article
- Flexible Docking of Cyclic Peptides to Proteins Using CABS-dock.Journal of chemical theory and computation · 2025Article
- Structure prediction of linear and cyclic peptides using CABS-flex.Briefings in bioinformatics · 2024Article
- Integrative modeling of diverse protein-peptide systems using CABS-dock.PLoS computational biology · 2023Article
- Computer- and NMR-Aided Design of Small-Molecule Inhibitors of the Hub1 Protein.Molecules (Basel, Switzerland) · 2022Article
- 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
- Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations.International journal of molecular sciences · 2021Article
- Molecular Dynamics Scoring of Protein-Peptide Models Derived from Coarse-Grained Docking.Molecules (Basel, Switzerland) · 2021Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The structural description of peptide ligands bound to G protein-coupled receptors (GPCRs) is important for the discovery of new drugs and deeper understanding of the molecular mechanisms of life. Here we describe a three-stage protocol for the molecular docking of peptides to GPCRs using a set of different programs: (1) CABS-dock for docking fully flexible peptides; (2) PD2 method for the reconstruction of atomistic structures from C-alpha traces provided by CABS-dock and (3) Rosetta FlexPepDock for the refinement of protein-peptide complex structures and model scoring. We evaluated the proposed protocol on the set of seven different GPCR-peptide complexes (including one containing a cyclic peptide), for which crystallographic structures are available. We show that CABS-dock produces high resolution models in the sets of top-scored models. These sets of models, after reconstruction to all-atom representation, can be further improved by Rosetta high-resolution refinement and/or minimization, leading in most of the cases to sub-Angstrom accuracy in terms of interface root-mean-square-deviation measure.
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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.