ArticleNature communications2020
Protein-ligand binding with the coarse-grained Martini model.
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 97 papers.
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Who cites it
97 citing papers in PubMed.
- A membrane-disruptive action of VBIT-4 challenges its role as a widely used VDAC1 oligomerization inhibitor.eLife · 2026Article
- SMartini: automated small molecule parametrization for Martini 3 force field.bioRxiv : the preprint server for biology · 2026Article
- Molecular Mechanisms of KIT Receptor Dimerization and Oncogenic Activation Revealed by Multiscale Simulations.Journal of chemical information and modeling · 2026Article
- In vitro and in silico modelling of ROS1-positive non-small cell lung cancer reveals fusion-dependent tyrosine kinase inhibitor responses.Molecular oncology · 2026Article
- GC-MS and GC-IMS Comprehensive Analysis of Volatile Compounds in the Peel and Pulp of Six Lemon Varieties and Their Interactions with Olfactory Receptors: Molecular Docking and Molecular Dynamics Simulations Studies.Foods (Basel, Switzerland) · 2026Article
- Martini Mapper: An Automated Fragment-Based Mapping Algorithm for Developing Coarse-Grained Models within the Martini 3 Framework.Journal of chemical information and modeling · 2026Article
- Effects of Liposome Composition and Size on Protein Corona Formation: Competitive Replacement of Abundant Proteins by High-Affinity Proteins on the Liposome Surface.Advanced healthcare materials · 2026Article
- Bridging Scales: Coarse-Grained Protein Models in Computational Biology.Advances in experimental medicine and biology · 2026Review
- Enzymatic Synthesis of β-lactam Antibiotics: From Enzyme Dataset Construction to Action Mechanism and Semi-Rational Design.Current protein & peptide science · 2026Review
- Identifying and Characterizing Lipid-Binding Cavities in Lipid Transfer Proteins With CG-MD Simulations.Bio-protocol · 2025Article
- Article
- Identification of potential natural BCL-2 inhibitors for leukemia through an integrated virtual screening approach.BMC pharmacology & toxicology · 2025Article
- Automated parametrization of small molecules within the Martini 3 coarse-grained model guided by experimental log P values.Scientific reports · 2025Article
- Challenges and opportunities in computational studies for lipid nanoparticle development.npj drug discovery · 2025Review
- A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations.Journal of chemical information and modeling · 2025Article
- Protein dimerization in 2D vs 3D: Geometric allostery enhances binding affinity.The Journal of chemical physics · 2025Article
- Probing the microRNA landscape in cadmium chloride induced renal toxicity through an in silico approach.Scientific reports · 2025Article
- Microtubules in Martini: Parameterizing a heterogeneous elastic-network towards a mechanically accurate microtubule.PNAS nexus · 2025Article
- Native globular ferritin nanopore sensor.Nature communications · 2025Article
- GōMartini 3: From large conformational changes in proteins to environmental bias corrections.Nature communications · 2025Article
37 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The detailed understanding of the binding of small molecules to proteins is the key for the development of novel drugs or to increase the acceptance of substrates by enzymes. Nowadays, computer-aided design of protein-ligand binding is an important tool to accomplish this task. Current approaches typically rely on high-throughput docking essays or computationally expensive atomistic molecular dynamics simulations. Here, we present an approach to use the recently re-parametrized coarse-grained Martini model to perform unbiased millisecond sampling of protein-ligand interactions of small drug-like molecules. Remarkably, we achieve high accuracy without the need of any a priori knowledge of binding pockets or pathways. Our approach is applied to a range of systems from the well-characterized T4 lysozyme over members of the GPCR family and nuclear receptors to a variety of enzymes. The presented results open the way to high-throughput screening of ligand libraries or protein mutations using the coarse-grained Martini model.
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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.