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[Related PubMed/MEDLINE]
Total Number of Papers: 65
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| No. |
Year |
Title |
Co-occurring Abbreviation |
| 1 |
2020 |
Martini Force Field for Protonated Polyethyleneimine. |
CG, FF, PEI |
| 2 |
2020 |
Molecular characterization of the outer membrane of Pseudomonas aeruginosa. |
CG, LPS, MD, OM |
| 3 |
2019 |
Analysis of local density potentials. |
CG, LD, MS-CG |
| 4 |
2019 |
Backmapping from Multiresolution Coarse-Grained Models to Atomic Structures of Large Biomolecules by Restrained Molecular Dynamics Simulations Using Bayesian Inference. |
CG, MD |
| 5 |
2019 |
Computational simulations of TNF receptor oligomerization on plasma membrane. |
CG, MD, TNFR1, TNFs |
| 6 |
2019 |
Curvature effect and stabilize ruptured membrane of BAX derived peptide studied by molecular dynamics simulations. |
CG, TMD |
| 7 |
2019 |
Curvature induction and sensing of the F-BAR protein Pacsin1 on lipid membranes via molecular dynamics simulations. |
CG, F-BAR |
| 8 |
2019 |
Effects of Ether Linkage on Membrane Dipole Potential and Cholesterol Flip-Flop Motion in Lipid Bilayer Membranes. |
CG |
| 9 |
2019 |
Top-down Multiscale Approach To Simulate Peptide Self-Assembly from Monomers. |
CG |
| 10 |
2018 |
Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field. |
CG, DOPC, DPPC, MD, Tm |
| 11 |
2018 |
Disease-related metabolites affect protein-nanoparticle interactions. |
CG, MD, NPs |
| 12 |
2018 |
Energy Renormalization Method for the Coarse-Graining of Polymer Viscoelasticity. |
CG, ER, GF, PB, PS |
| 13 |
2018 |
Persistence Length, End-to-End Distance, and Structure of Coarse-Grained Polymers. |
CG, PE, PTFE |
| 14 |
2018 |
Reconstruction of Atomistic Structures from Coarse-Grained Models for Protein-DNA Complexes. |
CG |
| 15 |
2018 |
Theoretical approaches for dynamical ordering of biomolecular systems. |
CG, MD, QM, QM/MM |
| 16 |
2018 |
Towards a coarse-grained model of the peptoid backbone: the case of N,N-dimethylacetamide. |
CG, DMA |
| 17 |
2017 |
Effects of Coarse Graining and Saturation of Hydrocarbon Chains on Structure and Dynamics of Simulated Lipid Molecules. |
CG, UA |
| 18 |
2017 |
Extending pressure-matching to inhomogeneous systems via local-density potentials. |
EOS |
| 19 |
2017 |
Modeling of low temperature adsorption of hydrogen in carbon nanopores. |
UA |
| 20 |
2017 |
Reduced Point Charge Models of Proteins: Effect of Protein-Water Interactions in Molecular Dynamics Simulations of Ubiquitin Systems. |
CG, FF, RPCM |
| 21 |
2017 |
Role of Dynamic Heterogeneities in Ionic Liquids: Insights from All-Atom and Coarse-Grained Molecular Dynamics Simulation Studies. |
CG |
| 22 |
2017 |
The orientation and stability of the GPCR-Arrestin complex in a lipid bilayer. |
CG, GPCRs |
| 23 |
2017 |
The unfolding mechanism of monomeric mutant SOD1 by simulated force spectroscopy. |
HA-Go, SOD1 |
| 24 |
2017 |
Transferable coarse-grained model for perfluorosulfonic acid polymer membranes. |
CG, IBI, MD, PFSA, SDK |
| 25 |
2016 |
As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy. |
AWSEM |
| 26 |
2016 |
Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures. |
CG |
| 27 |
2016 |
Estimation of Liposome Penetration Barriers of Drug Molecules with All-Atom and Coarse-Grained Models. |
5-ALA, CG |
| 28 |
2016 |
Multiscale design of coarse-grained elastic network-based potentials for the mu opioid receptor. |
CG, ENM, FF, GPCR, MD, muOR, NMA |
| 29 |
2016 |
Simulation of High Density Lipoprotein Behavior on a Few Layer Graphene Undergoing Non-Uniform Mechanical Load. |
CG, CNT, DPPC, HDL, SWNT |
| 30 |
2016 |
Systematic Generation of Anisotropic Coarse-Grained Lennard-Jones Potentials and Their Application to Ordered Soft Matter. |
CG, LoD, vdW |
| 31 |
2016 |
Van der Waals Perspective on Coarse-Graining: Progress toward Solving Representability and Transferability Problems. |
CG, PMF |
| 32 |
2015 |
Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids. |
CG, PMF |
| 33 |
2015 |
Coarse-grained model of glycosaminoglycans. |
CG, GAGs, MD |
| 34 |
2015 |
Exploring LacI-DNA dynamics by multiscale simulations using the SIRAH force field. |
CG, LacI |
| 35 |
2015 |
Molecular dynamics methods to predict peptide locations in membranes: LAH4 as a stringent test case. |
CG, PMF |
| 36 |
2015 |
On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer. |
CG, MD, POPC |
| 37 |
2014 |
Investigation of coarse-grained mappings via an iterative generalized Yvon-Born-Green method. |
CG, g-YBG, MS-CG, RDFs |
| 38 |
2014 |
Multi-scale ensemble modeling of modular proteins with intrinsically disordered linker regions: application to p53. |
CG, IDRs, MD, SAXS |
| 39 |
2014 |
Multiscale molecular dynamics simulations of sodium dodecyl sulfate micelles: from coarse-grained to all-atom resolution. |
CG, MD, QM, SDS, UA |
| 40 |
2014 |
Nanomechanics of beta-rich proteins related to neuronal disorders studied by AFM, all-atom and coarse-grained MD methods. |
AFM, CG MD, MD |
| 41 |
2014 |
RESPAC: Method to Determine Partial Charges in Coarse-Grained Protein Model and Its Application to DNA-Binding Proteins. |
CG, RESP |
| 42 |
2013 |
Comparison of two simulation methods to compute solvation free energies and partition coefficients. |
AAD, EE, OPLS, SPC/E, TI |
| 43 |
2013 |
Effect of arginine-rich peptide length on the structure and binding strength of siRNA-peptide complexes. |
Arg, CG, MD |
| 44 |
2013 |
Improved coarse-grained model for molecular-dynamics simulations of water nucleation. |
CG |
| 45 |
2013 |
Insertion of the Ca⁺-independent phospholipase A₂ into a phospholipid bilayer via coarse-grained and atomistic molecular dynamics simulations. |
CG, DXMS, MD |
| 46 |
2013 |
Molecular energetics in the capsomere of virus-like particle revealed by molecular dynamics simulations. |
MD, MM-PBSA, MPV, VLPs |
| 47 |
2013 |
SAFT-gamma force field for the simulation of molecular fluids: 2. Coarse-grained models of greenhouse gases, refrigerants, and long alkanes. |
CG, EOS, UA |
| 48 |
2012 |
Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining. |
--- |
| 49 |
2012 |
Computer simulation studies of self-assembling macromolecules. |
CG, MD |
| 50 |
2012 |
Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units. |
CG, GBSA, GPU, LBMC |
| 51 |
2012 |
[Non-commutative geometrical drug discovery--the principle of geometrical regulation]. |
CG, QC |
| 52 |
2011 |
A hybrid all-atom/coarse grain model for multiscale simulations of DNA. |
--- |
| 53 |
2011 |
Coarse-grained modeling study of nonpeptide RGD ligand density and PEG molecular weight on the conformation of poly(gamma-glutamyl-glutamate) paclitaxel conjugates. |
CG, MD, MW, PGG-PTX-PEG-npRGD |
| 54 |
2011 |
Modification of Martini force field for molecular dynamics simulation of hydrophobic charge induction chromatography of lysozyme. |
CG, HCIC, MD |
| 55 |
2010 |
Characterization of a clinical polymer-drug conjugate using multiscale modeling. |
CG, MD, PGG-PTX, PTX |
| 56 |
2010 |
Coarse-grained molecular dynamics of tetrameric transmembrane peptide bundles within a lipid bilayer. |
CG, MD |
| 57 |
2010 |
Parametrization and application of a coarse grained force field for benzene/fullerene interactions with lipids. |
CG, MD |
| 58 |
2009 |
A dual-scale approach toward structure prediction of retinal proteins. |
bR, CG, HR, RPs, SRI, SRII |
| 59 |
2009 |
A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids. |
CG, LJ, SASA |
| 60 |
2009 |
Coarse-grained molecular dynamics study of cyclic peptide nanotube insertion into a lipid bilayer. |
CG, MD |
| 61 |
2009 |
Structure, dynamics, and ion conductance of the phospholamban pentamer. |
CG, PLN |
| 62 |
2008 |
Packing of transmembrane helices in bacteriorhodopsin folding: structure and thermodynamics. |
bR, CG, HMPs, RMSD |
| 63 |
2008 |
Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study. |
CG |
| 64 |
2008 |
Reconstructing atomistic detail for coarse-grained models with resolution exchange. |
CG |
| 65 |
2006 |
A novel united-atom force field for imidazolium-based ionic liquids. |
UA |
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