ArticleJournal of molecular modeling2017
Modeling DMPC lipid membranes with SIRAH force-field.
Article in Journal of molecular modeling, 2017. 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.
- Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery.Molecular pharmaceutics · 2025Review
- Molecular dynamics simulation of apolipoprotein E3 lipid nanodiscs.Biochimica et biophysica acta. Biomembranes · 2024Article
- Article
- Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?Bioscience reports · 2022Article
- Paired Simulations and Experimental Investigations into the Calcium-Dependent Conformation of Albumin.Journal of chemical information and modeling · 2022Article
- The automated optimisation of a coarse-grained force field using free energy data.Physical chemistry chemical physics : PCCP · 2021Article
- Identification and Characterization of Specific Protein-Lipid Interactions Using Molecular Simulation.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane.Biophysical journal · 2020Article
- Computer simulations of protein-membrane systems.Progress in molecular biology and translational science · 2020Article
- From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field.Interface focus · 2019Review
- Computational Modeling of Realistic Cell Membranes.Chemical reviews · 2019Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Coarse-grained simulation schemes are increasingly gaining popularity in the scientific community because of the significant speed up granted, allowing a considerable expansion of the accessible time and size scales accessible to molecular simulations. However, the number of compatible force fields capable of representing ensembles containing different molecular species (i.e., Protein, DNA, etc) is still limited. Here, we present a set of parameters and simplified representation for lipids compatible with the SIRAH force field for coarse-grained simulations ( http://www.sirahff.com ). We show that the present model not only achieves a correct reproduction of structural parameters as area per lipid and thickness, but also dynamic descriptors such as diffusion coefficient, order parameters, and proper temperature driven variations. Adding phospholipid membranes to the existing aqueous solution, protein and DNA representations of the SIRAH force field permit considering the most common problems tackled by the biomolecular simulation community.
Indexed as
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28799119What OpenQuestion holds
Registered trials
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.