K-Means Clustering Coarse-Graining (KMC-CG): A Next Generation Methodology for Determining Optimal Coarse-Grained Mappings of Large Biomolecules

J Wu, W Xue, GA Voth - Journal of Chemical Theory and …, 2023 - ACS Publications
Coarse-grained (CG) molecular dynamics (MD) has become a method of choice for
simulating various large scale biomolecular processes; therefore, the systematic definition of …

A systematic methodology for defining coarse-grained sites in large biomolecules

Z Zhang, L Lu, WG Noid, V Krishna, J Pfaendtner… - Biophysical journal, 2008 - cell.com
Coarse-grained (CG) models of biomolecules have recently attracted considerable interest
because they enable the simulation of complex biological systems on length-scales and …

A new algorithm for construction of coarse‐grained sites of large biomolecules

M Li, JZH Zhang, F Xia - Journal of Computational Chemistry, 2016 - Wiley Online Library
The development of coarse‐grained (CG) models for large biomolecules remains a
challenge in multiscale simulations, including a rigorous definition of CG representations for …

A review of coarse-grained molecular dynamics techniques to access extended spatial and temporal scales in biomolecular simulations

BA Merchant, JD Madura - Annual Reports in Computational Chemistry, 2011 - Elsevier
The study of very large biomolecular systems over extended spatial and temporal scales is
being accomplished through the use of coarse-grained (CG) models. The successes of …

[HTML][HTML] Encoding and selecting coarse-grain mapping operators with hierarchical graphs

M Chakraborty, C Xu, AD White - The Journal of Chemical Physics, 2018 - pubs.aip.org
Coarse-grained (CG) molecular dynamics (MD) can simulate systems inaccessible to fine-
grained (FG) MD simulations. A CG simulation decreases the degrees of freedom by …

Graph-based approach to systematic molecular coarse-graining

MA Webb, JY Delannoy… - Journal of chemical theory …, 2018 - ACS Publications
A novel methodology is introduced here to generate coarse-grained (CG) representations of
molecular models for simulations. The proposed strategy relies on basic graph-theoretic …

Backmapping from multiresolution coarse-grained models to atomic structures of large biomolecules by restrained molecular dynamics simulations using bayesian …

J Peng, C Yuan, R Ma, Z Zhang - Journal of chemical theory and …, 2019 - ACS Publications
Coarse-grained (CG) simulations have allowed access to larger length scales and longer
time scales in the study of the dynamic processes of large biomolecules than all-atom (AA) …

Reactive coarse-grained molecular dynamics

T Dannenhoffer-Lafage, GA Voth - Journal of Chemical Theory …, 2020 - ACS Publications
Coarse-grained (CG) models have allowed for the study of long time and length scale
properties of a variety of systems. However, when a system undergoes chemical reactions …

Performance comparison of systematic methods for rigorous definition of coarse-grained sites of large biomolecules

Y Zhang, Z Cao, JZ Zhang, F Xia - Journal of Chemical Information …, 2017 - ACS Publications
Construction of coarse-grained (CG) models for large biomolecules used for multiscale
simulations demands a rigorous definition of CG sites for them. Several coarse-graining …

Constructing optimal coarse-grained sites of huge biomolecules by fluctuation maximization

M Li, JZ Zhang, F Xia - Journal of chemical theory and …, 2016 - ACS Publications
Coarse-grained (CG) models are valuable tools for the study of functions of large
biomolecules on large length and time scales. The definition of CG representations for huge …