ArticleJournal of chemical information and modeling2014
CHARMM-GUI PACE CG Builder for solution, micelle, and bilayer coarse-grained simulations.
Article in Journal of chemical information and modeling, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
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- Exploring the Properties of Curved Lipid Membranes: Comparative Analysis of Atomistic and Coarse-Grained Force Fields.The journal of physical chemistry. B · 2024Article
- Unraveling the Molecular Dance: Insights into TREM2/DAP12 Complex Formation in Alzheimer's Disease through Molecular Dynamics Simulations.ACS omega · 2024Article
- First report on exploration of structural features of natural compounds (NPACT database) for anti-breast cancer activity (MCF-7): QSAR-based virtual screening, molecular docking, ADMET, MD simulation, and DFT studies.In silico pharmacology · 2024Article
- pyCHARMM: Embedding CHARMM Functionality in a Python Framework.Journal of chemical theory and computation · 2023Article
- Effect of Slp4-a on Membrane Bending During Prefusion of Vesicles in Blood-Brain Barrier.Journal of biomechanical engineering · 2023Article
- Molecular Dynamics Simulations of Curved Lipid Membranes.International journal of molecular sciences · 2022Review
- Molecular modelling of the HCMV IL-10 protein isoforms and analysis of their interaction with the human IL-10 receptor.PloS one · 2022Article
- Hybrid resolution molecular dynamics simulations of amyloid proteins interacting with membranes.Methods (San Diego, Calif.) · 2022Article
- Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Effect of Calcium ion on synaptotagmin-like protein during pre-fusion of vesicle for exocytosis in blood-brain barrier.Biochemistry and biophysics reports · 2020Article
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Authors and funding
6 authors.
Funding
Abstract
Coarse-grained (CG) and multiscale simulations are widely used to study large biological systems. However, preparing the simulation system is time-consuming when the system has multiple components, because each component must be arranged carefully as in protein/micelle or protein/bilayer systems. We have developed CHARMM-GUI PACE CG Builder for building solution, micelle, and bilayer systems using the PACE force field, a united-atom (UA) model for proteins, and the Martini CG force field for water, ions, and lipids. The robustness of PACE CG Builder is validated by simulations of various systems in solution (α3D, fibronectin, and lysozyme), micelles (Pf1, DAP12-NKG2C, OmpA, and DHPC-only micelle), and bilayers (GpA, OmpA, VDAC, MscL, OmpF, and lipid-only bilayers for six lipids). The micelle's radius of gyration, the bilayer thickness, and the per-lipid area in bilayers are comparable to the values from previous all-atom and CG simulations. Most tested proteins have root-mean squared deviations of less than 3 Å. We expect PACE CG Builder to be a useful tool for modeling/refining large, complex biological systems at the mixed UA/CG level.
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