ArticleNature communications2020
Integrative modeling of membrane-associated protein assemblies.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Macrophage-derived cathepsin B disrupts intestinal tight junctions through occludin degradation and promotes alcohol-associated liver disease.Journal of hepatology · 2026Article
- Integrating AlphaFold2, RoseTTAFold2, and HADDOCK to refine Protein-Protein Interaction (PPI) candidate selection: A case study with ZWINT.Biochemistry and biophysics reports · 2026Article
- Identification of 14-3-3 Proteins as Binding Partners of TRP Channels.Journal of chemical information and modeling · 2026Article
- Inactive ryanodine receptors sustain lysosomal availability for autophagy by promoting ER-lysosomal contact site formation.Nature communications · 2026Article
- Development and Functional Characterization of Recombinant Mussel Adhesive Protein for Anti-Oxidative and Anti-Aging Therapeutic Applications.International journal of molecular sciences · 2025Article
- Role of adiponectin and its receptors AdipoR1/2 in inflammatory bowel disease.Cell communication and signaling : CCS · 2025Review
- Article
- Advancing Membrane-Associated Protein Docking with Improved Sampling and Scoring in Rosetta.Journal of chemical theory and computation · 2024Article
- Tuning architectural organization of eukaryotic P450 system to boost bioproduction in Escherichia coli.Nature communications · 2024Article
- The HADDOCK2.4 web server for integrative modeling of biomolecular complexes.Nature protocols · 2024Review
- Inhibitory Potential of the Truncated Isoforms on Glutamate Transporter Oligomerization Identified by Computational Analysis of Gene-Centric Isoform Maps.Pharmaceutical research · 2024Article
- Advancing membrane-associated protein docking with improved sampling and scoring in Rosetta.bioRxiv : the preprint server for biology · 2024Article
- Pannexin-3 stabilizes the transcription factor Bcl6 in a channel-independent manner to protect against vascular oxidative stress.Science signaling · 2024Article
- Transmembrane proteins in grape immunity: current knowledge and methodological advances.Frontiers in plant science · 2024Review
- The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions.Nucleic acids research · 2023Article
- Potential Common Mechanisms of Cytotoxicity Induced by Amide Herbicides via TRPA1 Channel Activation.International journal of environmental research and public health · 2022Article
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- VARIDT 2.0: structural variability of drug transporter.Nucleic acids research · 2022Article
- Towards design of drugs and delivery systems with the Martini coarse-grained model.QRB discovery · 2022Review
- Dependence of Protein Structure on Environment: FOD Model Applied to Membrane Proteins.Membranes · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Membrane proteins are among the most challenging systems to study with experimental structural biology techniques. The increased number of deposited structures of membrane proteins has opened the route to modeling their complexes by methods such as docking. Here, we present an integrative computational protocol for the modeling of membrane-associated protein assemblies. The information encoded by the membrane is represented by artificial beads, which allow targeting of the docking toward the binding-competent regions. It combines efficient, artificial intelligence-based rigid-body docking by LightDock with a flexible final refinement with HADDOCK to remove potential clashes at the interface. We demonstrate the performance of this protocol on eighteen membrane-associated complexes, whose interface lies between the membrane and either the cytosolic or periplasmic regions. In addition, we provide a comparison to another state-of-the-art docking software, ZDOCK. This protocol should shed light on the still dark fraction of the interactome consisting of membrane proteins.
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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.