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 …
Coarse-grained models for proteins
V Tozzini - Current opinion in structural biology, 2005 - Elsevier
Coarse-grained models for proteins and biomolecular aggregates have recently enjoyed
renewed interest. Coarse-grained representations combined with enhanced computer …
renewed interest. Coarse-grained representations combined with enhanced computer …
Speeding molecular recognition by using the folding funnel: the fly-casting mechanism
BA Shoemaker, JJ Portman… - Proceedings of the …, 2000 - National Acad Sciences
Protein folding and binding are kindred processes. Many proteins in the cell are unfolded, so
folding and function are coupled. This paper investigates how binding kinetics is influenced …
folding and function are coupled. This paper investigates how binding kinetics is influenced …
On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
H Fukunishi, O Watanabe, S Takada - The Journal of chemical physics, 2002 - pubs.aip.org
Predicting protein structure solely from its amino acid sequence has long been a grand
challenge in structural biology and theoretical chemistry. 1–3 Exponentially increasing the …
challenge in structural biology and theoretical chemistry. 1–3 Exponentially increasing the …
An all‐atom structure‐based potential for proteins: bridging minimal models with all‐atom empirical forcefields
Protein dynamics take place on many time and length scales. Coarse‐grained structure‐
based \bf(G\overlineo) models utilize the funneled energy landscape theory of protein …
based \bf(G\overlineo) models utilize the funneled energy landscape theory of protein …
Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse
The interplay between structure-search of the native structure and desolvation in protein
folding has been explored using a minimalist model. These results support a folding …
folding has been explored using a minimalist model. These results support a folding …
Molecular mechanics
K Vanommeslaeghe, O Guvench - Current pharmaceutical …, 2014 - ingentaconnect.com
Molecular Mechanics (MM) force fields are the methods of choice for protein simulations,
which are essential in the study of conformational flexibility. Given the importance of protein …
which are essential in the study of conformational flexibility. Given the importance of protein …
[HTML][HTML] Applications of molecular dynamics simulation in structure prediction of peptides and proteins
H Geng, F Chen, J Ye, F Jiang - Computational and structural …, 2019 - Elsevier
Compared with rapid accumulation of protein sequences from high-throughput DNA
sequencing, obtaining experimental 3D structures of proteins is still much more difficult …
sequencing, obtaining experimental 3D structures of proteins is still much more difficult …
Mechanism for the α‐helix to β‐hairpin transition
F Ding, JM Borreguero, SV Buldyrey… - Proteins: Structure …, 2003 - Wiley Online Library
The aggregation of α‐helix‐rich proteins into β‐sheet‐rich amyloid fibrils is associated with
fatal diseases, such as Alzheimer's disease and prion disease. During an aggregation …
fatal diseases, such as Alzheimer's disease and prion disease. During an aggregation …
In silico study of amyloid β-protein folding and oligomerization
Experimental findings suggest that oligomeric forms of the amyloid β protein (Aβ) play a
critical role in Alzheimer's disease. Thus, elucidating their structure and the mechanisms of …
critical role in Alzheimer's disease. Thus, elucidating their structure and the mechanisms of …