ArticleFrontiers in molecular biosciences2021
Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations.
Article in Frontiers in molecular biosciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Bridging Scales: Coarse-Grained Protein Models in Computational Biology.Advances in experimental medicine and biology · 2026Review
- Article
- Martini 3 coarse-grained model of enzymes: Framework with validation by all-atom simulations and x-ray diffraction measurements.The Journal of chemical physics · 2025Article
- Minute-timescale free-energy calculations reveal a pseudo-active state in the adenosine AChem · 2024Article
- Deep Learning-Based Classification of Histone-DNA Interactions Using Drying Droplet Patterns.Small science · 2024Article
- A millisecond coarse-grained simulation approach to decipher allosteric cannabinoid binding at the glycine receptor α1.Nature communications · 2024Article
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Identification of inhibitors targeting the energy-coupling factor (ECF) transporters.Communications biology · 2023Article
- Structural basis of dimerization of chemokine receptors CCR5 and CXCR4.Nature communications · 2023Article
- Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness.Journal of chemical theory and computation · 2023Review
- Differential interactions of resting, activated, and desensitized states of the α7 nicotinic acetylcholine receptor with lipidic modulators.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Towards design of drugs and delivery systems with the Martini coarse-grained model.QRB discovery · 2022Review
- Understanding insulin and its receptor from their three-dimensional structures.Molecular metabolism · 2021Review
- Improving Small-Molecule Force Field Parameters in Ligand Binding Studies.Frontiers in molecular biosciences · 2021Article
- Article
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Authors and funding
5 authors.
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Abstract
Molecular docking is central to rational drug design. Current docking techniques suffer, however, from limitations in protein flexibility and solvation models and by the use of simplified scoring functions. All-atom molecular dynamics simulations, on the other hand, feature a realistic representation of protein flexibility and solvent, but require knowledge of the binding site. Recently we showed that coarse-grained molecular dynamics simulations, based on the most recent version of the Martini force field, can be used to predict protein/ligand binding sites and pathways, without requiring any
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