Coarse-grained protein models and their applications

S Kmiecik, D Gront, M Kolinski, L Wieteska… - Chemical …, 2016‏ - ACS Publications
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 …

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 …

On develo** coarse-grained models for biomolecular simulation: a review

S Riniker, JR Allison, WF van Gunsteren - … Chemistry Chemical Physics, 2012‏ - pubs.rsc.org
So-called coarse-grained models are a popular type of model for accessing long time scales
in simulations of biomolecular processes. Such models are coarse-grained with respect to …

Modeling and simulation of ion channels

C Maffeo, S Bhattacharya, J Yoo, D Wells… - Chemical …, 2012‏ - ACS Publications
Transport of ions through pores in membranes is a process of fundamental importance to
cell biology. In living organisms, such transport is facilitated by ion channels that utilize the …

From coarse grained to atomistic: a serial multiscale approach to membrane protein simulations

PJ Stansfeld, MSP Sansom - Journal of chemical theory and …, 2011‏ - ACS Publications
Coarse-grained molecular dynamics provides a means for simulating the assembly and the
interactions of membrane protein/lipid complexes at a reduced level of representation …

The role of cholesterol in M2 clustering and viral budding explained

D Kolokouris, IE Kalenderoglou… - Journal of Chemical …, 2024‏ - ACS Publications
The influenza A M2 homotetrameric channel consists of four transmembrane (TM) and four
amphipathic helices (AHs). This viral proton channel is suggested to form clusters in the …

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

AJ Rzepiela, M Louhivuori, C Peter… - Physical Chemistry …, 2011‏ - pubs.rsc.org
Hybrid simulations, in which part of the system is represented at atomic resolution and the
remaining part at a reduced, coarse-grained, level offer a powerful way to combine the …

Reconstruction of atomistic details from coarse‐grained structures

AJ Rzepiela, LV Schäfer, N Goga… - Journal of …, 2010‏ - Wiley Online Library
We present an algorithm to reconstruct atomistic structures from their corresponding coarse‐
grained (CG) representations and its implementation into the freely available molecular …

A massively parallel infrastructure for adaptive multiscale simulations: modeling RAS initiation pathway for cancer

F Di Natale, H Bhatia, TS Carpenter, C Neale… - Proceedings of the …, 2019‏ - dl.acm.org
Computational models can define the functional dynamics of complex systems in
exceptional detail. However, many modeling studies face seemingly incommensurate …

Structure and Mechanism of the Influenza A M218–60 Dimer of Dimers

LB Andreas, M Reese, MT Eddy, V Gelev… - Journal of the …, 2015‏ - ACS Publications
We report a magic angle spinning (MAS) NMR structure of the drug-resistant S31N mutation
of M218–60 from Influenza A. The protein was dispersed in diphytanoyl-sn-glycero-3 …