GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems
Residue-level coarse-grained (CG) molecular dynamics (MD) simulation is widely used to
investigate slow biological processes that involve multiple proteins, nucleic acids, and their …
investigate slow biological processes that involve multiple proteins, nucleic acids, and their …
Evaluation of Essential Dynamics and Fixed-Length Coarse Graining for Multidomain Proteins
For multiscale modeling of biomolecules, reliable coarse-grained (CG) models can offer
great potential to simulate larger temporal and spatial scales than traditional all-atom (AA) …
great potential to simulate larger temporal and spatial scales than traditional all-atom (AA) …
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
Residue-level coarse-grained (CG) models have become one of the most popular tools in
biomolecular simulations in the trade-off between modeling accuracy and computational …
biomolecular simulations in the trade-off between modeling accuracy and computational …
Recent advances in transferable coarse-grained modeling of proteins
P Kar, M Feig - Advances in protein chemistry and structural biology, 2014 - Elsevier
Computer simulations are indispensable tools for studying the structure and dynamics of
biological macromolecules. Biochemical processes occur on different scales of length and …
biological macromolecules. Biochemical processes occur on different scales of length and …
Coarse-grained molecular simulations of large biomolecules
S Takada - Current opinion in structural biology, 2012 - Elsevier
Recently, we saw a dramatic increase in the number of researches that rely on coarse-
grained (CG) simulations for large biomolecules. Here, first, we briefly describe recently …
grained (CG) simulations for large biomolecules. Here, first, we briefly describe recently …
Backmapping from multiresolution coarse-grained models to atomic structures of large biomolecules by restrained molecular dynamics simulations using bayesian …
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) …
time scales in the study of the dynamic processes of large biomolecules than all-atom (AA) …
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 …
because they enable the simulation of complex biological systems on length-scales and …
Modeling structural dynamics of biomolecular complexes by coarse-grained molecular simulations
Conspectus Due to hierarchic nature of biomolecular systems, their computational modeling
calls for multiscale approaches, in which coarse-grained (CG) simulations are used to …
calls for multiscale approaches, in which coarse-grained (CG) simulations are used to …
Advanced sampling methods for multiscale simulation of disordered proteins and dynamic interactions
Intrinsically disordered proteins (IDPs) are highly prevalent and play important roles in
biology and human diseases. It is now also recognized that many IDPs remain dynamic …
biology and human diseases. It is now also recognized that many IDPs remain dynamic …
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 …
being accomplished through the use of coarse-grained (CG) models. The successes of …