Bottom-up coarse-graining: Principles and perspectives

J **, AJ Pak, AEP Durumeric, TD Loose… - Journal of chemical …, 2022 - ACS Publications
Large-scale computational molecular models provide scientists a means to investigate the
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …

Perspective on the Martini model

SJ Marrink, DP Tieleman - Chemical Society Reviews, 2013 - pubs.rsc.org
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 …

The MARTINI coarse-grained force field: extension to proteins

L Monticelli, SK Kandasamy, X Periole… - Journal of chemical …, 2008 - ACS Publications
Many biologically interesting phenomena occur on a time scale that is too long to be studied
by atomistic simulations. These phenomena include the dynamics of large proteins and self …

Coarse-graining methods for computational biology

MG Saunders, GA Voth - Annual review of biophysics, 2013 - annualreviews.org
Connecting the molecular world to biology requires understanding how molecular-scale
dynamics propagate upward in scale to define the function of biological structures. To …

Characterization of lipid–protein interactions and lipid-mediated modulation of membrane protein function through molecular simulation

MP Muller, T Jiang, C Sun, M Lihan, S Pant… - Chemical …, 2019 - ACS Publications
The cellular membrane constitutes one of the most fundamental compartments of a living
cell, where key processes such as selective transport of material and exchange of …

[BOOK][B] Coarse-graining of condensed phase and biomolecular systems

GA Voth - 2008 - taylorfrancis.com
Exploring recent developments in the field, Coarse-Graining of Condensed Phase and
Biomolecular Systems examines systematic ways of constructing coarse-grained …

Multiscale simulation of soft matter systems–from the atomistic to the coarse-grained level and back

C Peter, K Kremer - Soft Matter, 2009 - pubs.rsc.org
Many physical phenomena and properties of soft matter systems such as synthetic or
biological materials are governed by interactions and processes on a wide range of length …

Basic ingredients of free energy calculations: a review

CD Christ, AE Mark… - Journal of computational …, 2010 - Wiley Online Library
Methods to compute free energy differences between different states of a molecular system
are reviewed with the aim of identifying their basic ingredients and their utility when applied …

Multiscale simulation of soft matter: From scale bridging to adaptive resolution

M Praprotnik, LD Site, K Kremer - Annu. Rev. Phys. Chem., 2008 - annualreviews.org
The relation between atomistic chemical structure, molecular architecture, molecular weight,
and material properties is of basic concern in modern soft material science and includes …

Multiscale modeling of biomolecular systems: in serial and in parallel

GS Ayton, WG Noid, GA Voth - Current opinion in structural biology, 2007 - Elsevier
Considerable progress has been recently achieved in the multiscale modeling of complex
biological processes. Multiscale models have now investigated the structure and dynamics …