ArticleThe journal of physical chemistry. B2012
LIPID11: a modular framework for lipid simulations using amber.
Article in The journal of physical chemistry. B, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed.
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- Computer Simulations of Multidrug Efflux Pumps of the Resistance-Nodulation-Cell Division Superfamily.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Development of force field parameters for the atomic simulation of Mycobacterial membranes.Communications chemistry · 2025Article
- Unveiling the Interactions of Doxorubicin with the Lipid Components of Liposomes for Its Delivery.The journal of physical chemistry. B · 2025Article
- Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery.Molecular pharmaceutics · 2025Review
- Simulation of Linear and Cyclic Alkanes with Second-Order Møller-Plesset Perturbation Theory through Adaptive Force Matching.Journal of chemical theory and computation · 2024Article
- Identification of small molecular inhibitors of SIRT3 by computational and biochemical approaches a potential target of breast cancer.Scientific reports · 2024Article
- Effect of Monovalent Cations on the Structure and Dynamics of Multimodal Chromatographic Surfaces.Langmuir : the ACS journal of surfaces and colloids · 2024Article
- Identification of new pharmacophore against SARS-CoV-2 spike protein by multi-fold computational and biochemical techniques.Scientific reports · 2024Article
- Biophysical Modelling for Insight into Oxygen Diffusion, Distribution, and Measurement.Advances in experimental medicine and biology · 2024Article
- Interaction of Macromolecular Chain with Phospholipid Membranes in Solutions: A Dissipative Particle Dynamics Simulation Study.Molecules (Basel, Switzerland) · 2023Article
- Expanding the Paradigm of Structure-Based Drug Design: Molecular Dynamics Simulations Support the Development of New Pyridine-Based Protein Kinase C-Targeted Agonists.Journal of medicinal chemistry · 2023Article
- Article
- Thermal site energy fluctuations in photosystem I: new insights from MD/QM/MM calculations.Chemical science · 2023Article
- On the Permeation of Polychlorinated Dibenzodioxins and Dibenzofurans through Lipid Membranes: Classical MD and Hybrid QM/MM-EDA Analysis.Membranes · 2022Article
- Lipid21: Complex Lipid Membrane Simulations with AMBER.Journal of chemical theory and computation · 2022Article
- Simulations of Kindlin-2 PIP binding domains reveal protonation-dependent membrane binding modes.Biophysical journal · 2021Article
- Structural Modelling of KCNQ1 and KCNH2 Double Mutant Proteins, Identified in Two Severe Long QT Syndrome Cases, Reveals New Insights into Cardiac Channelopathies.International journal of molecular sciences · 2021Article
- Article
4 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
Accurate simulation of complex lipid bilayers has long been a goal in condensed phase molecular dynamics (MD). Structure and function of membrane-bound proteins are highly dependent on the lipid bilayer environment and are challenging to study through experimental methods. Within Amber, there has been limited focus on lipid simulations, although some success has been seen with the use of the General Amber Force Field (GAFF). However, to date there are no dedicated Amber lipid force fields. In this paper we describe a new charge derivation strategy for lipids consistent with the Amber RESP approach and a new atom and residue naming and type convention. In the first instance, we have combined this approach with GAFF parameters. The result is LIPID11, a flexible, modular framework for the simulation of lipids that is fully compatible with the existing Amber force fields. The charge derivation procedure, capping strategy, and nomenclature for LIPID11, along with preliminary simulation results and a discussion of the planned long-term parameter development are presented here. Our findings suggest that LIPID11 is a modular framework feasible for phospholipids and a flexible starting point for the development of a comprehensive, Amber-compatible lipid force field.
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Registered trials
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