Bottom-up coarse-graining: Principles and perspectives
Large-scale computational molecular models provide scientists a means to investigate the
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …
Perspective: Advances, challenges, and insight for predictive coarse-grained models
WG Noid - The Journal of Physical Chemistry B, 2023 - ACS Publications
By averaging over atomic details, coarse-grained (CG) models provide profound
computational and conceptual advantages for studying soft materials. In particular, bottom …
computational and conceptual advantages for studying soft materials. In particular, bottom …
Ab initio protein structure assembly using continuous structure fragments and optimized knowledge‐based force field
Ab initio protein folding is one of the major unsolved problems in computational biology
owing to the difficulties in force field design and conformational search. We developed a …
owing to the difficulties in force field design and conformational search. We developed a …
Perspective: Coarse-grained models for biomolecular systems
WG Noid - The Journal of chemical physics, 2013 - pubs.aip.org
By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …
grained (CG) models provide significant computational and conceptual advantages with …
Pragmatic coarse-graining of proteins: models and applications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …
proteins with other molecules are often difficult to assess by experimental techniques …
[图书][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 …
Biomolecular Systems examines systematic ways of constructing coarse-grained …
Principal component analysis for protein folding dynamics
GG Maisuradze, A Liwo, HA Scheraga - Journal of molecular biology, 2009 - Elsevier
Protein folding is considered here by studying the dynamics of the folding of the triple β-
strand WW domain from the Formin-binding protein 28. Starting from the unfolded state and …
strand WW domain from the Formin-binding protein 28. Starting from the unfolded state and …
Significant progress in predicting the crystal structures of small organic molecules–a report on the fourth blind test
GM Day, TG Cooper, AJ Cruz-Cabeza… - … Section B: Structural …, 2009 - journals.iucr.org
We report on the organization and outcome of the fourth blind test of crystal structure
prediction, an international collaborative project organized to evaluate the present state in …
prediction, an international collaborative project organized to evaluate the present state in …
A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions
A Liwo, M Baranowski, C Czaplewski, E Gołaś… - Journal of molecular …, 2014 - Springer
A unified coarse-grained model of three major classes of biological molecules—proteins,
nucleic acids, and polysaccharides—has been developed. It is based on the observations …
nucleic acids, and polysaccharides—has been developed. It is based on the observations …
[HTML][HTML] The impact of resolution upon entropy and information in coarse-grained models
By eliminating unnecessary degrees of freedom, coarse-grained (CG) models tremendously
facilitate numerical calculations and theoretical analyses of complex phenomena. However …
facilitate numerical calculations and theoretical analyses of complex phenomena. However …