Enhanced sampling methods for molecular dynamics simulations
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …
molecular dynamics simulations and allow the sampling of larger portions of the …
Computational modeling of realistic cell membranes
Cell membranes contain a large variety of lipid types and are crowded with proteins,
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …
Coarse-grained protein models and their applications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …
remains difficult for many protein systems. It is mostly due to the size of protein …
Perspective on the Martini model
The Martini model, a coarse-grained force field for biomolecular simulations, has found a
broad range of applications since its release a decade ago. Based on a building block …
broad range of applications since its release a decade ago. Based on a building block …
Improved parameters for the martini coarse-grained protein force field
The Martini coarse-grained force field has been successfully used for simulating a wide
range of (bio) molecular systems. Recent progress in our ability to test the model against …
range of (bio) molecular systems. Recent progress in our ability to test the model against …
G protein–coupled receptor oligomerization revisited: functional and pharmacological perspectives
Most evidence indicates that, as for family CG protein–coupled receptors (GPCRs), family A
GPCRs form homo-and heteromers. Homodimers seem to be a predominant species, with …
GPCRs form homo-and heteromers. Homodimers seem to be a predominant species, with …
Principles and overview of sampling methods for modeling macromolecular structure and dynamics
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …
how macromolecules carry out their functions in the cell. Significant advances have been …
Excessive aggregation of membrane proteins in the Martini model
The coarse-grained Martini model is employed extensively to study membrane protein
oligomerization. While this approach is exceptionally promising given its computational …
oligomerization. While this approach is exceptionally promising given its computational …
Computational 'microscopy'of cellular membranes
Computational 'microscopy'refers to the use of computational resources to simulate the
dynamics of a molecular system. Tuned to cell membranes, this computational …
dynamics of a molecular system. Tuned to cell membranes, this computational …
What is the function of mitochondrial networks? A theoretical assessment of hypotheses and proposal for future research
Mitochondria can change their shape from discrete isolated organelles to a large continuous
reticulum. The cellular advantages underlying these fused networks are still incompletely …
reticulum. The cellular advantages underlying these fused networks are still incompletely …