Concepedia

A designer minimalistic model parallels the phase-separation-mediated assembly and biophysical cues of extracellular matrix

Xian Ning Xie, Tianjie Li, Linjie Ma, Jiahao Wu, Yajing Qi, Boguang Yang, Zhuo Li, Zhinan Yang, Kunyu Zhang, Zhiqin Chu,

Nature Chemistry · 2025 · 27 citations · 53 references

Concepts

Life SciencesBiologyCell BiologyBiomolecular ModelingCell-matrix AdhesionExtracellular MatrixExtracellular Matrix BiochemistryExtracellular Matrix BiologyMacromolecular AssemblyMacromolecular Assembly ModelingExtracellular Matrix AssemblyExtracellular Matrix CompositionExtracellular Matrix ModelingExtracellular Matrix OrganizationMatrix AssemblyMatrix BiochemistryMatrix-cell InteractionsPhase Separation In Self-assembly

References

53

VMD: Visual molecular dynamics

William Humphrey, Andrew Dalke, Klaus Schulten · Journal of Molecular Graphics · 1996 · 66.6K citations

Natural Sciences, Biophysics, Physics +12

Highly accurate protein structure prediction with AlphaFold

John Jumper, Alexander Pritzel, Tim Green et al. · Nature · 2021 · 45.2K citations · Full text

Life Sciences, Biochemistry, Bioinformatics +11

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

M Abraham, Teemu J. Murtola, Roland Schulz et al. · SoftwareX · 2015 · 26.8K citations · Full text

Computing, Computer Science, High-performance Computing +11

Polymorphic transitions in single crystals: A new molecular dynamics method

Michele Parrinello, A. Rahman · Journal of Applied Physics · 1981 · 20.2K citations

Natural Sciences, Chemistry, Physics +15

Canonical sampling through velocity rescaling

Giovanni Bussi, Davide Donadio, Michele Parrinello · The Journal of Chemical Physics · 2007 · 18.4K citations · Full text

Natural Sciences, Chemistry, Physics +17