The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems
The OPEP coarse-grained protein model has been applied to a wide range of applications
since its first release 15 years ago. The model, which combines energetic and structural …
since its first release 15 years ago. The model, which combines energetic and structural …
Protein aggregation: in silico algorithms and applications
Protein aggregation is a topic of immense interest to the scientific community due to its role
in several neurodegenerative diseases/disorders and industrial importance. Several in silico …
in several neurodegenerative diseases/disorders and industrial importance. Several in silico …
GROMACS in the cloud: A global supercomputer to speed up alchemical drug design
C Kutzner, C Kniep, A Cherian… - Journal of Chemical …, 2022 - ACS Publications
We assess costs and efficiency of state-of-the-art high-performance cloud computing and
compare the results to traditional on-premises compute clusters. Our use case is atomistic …
compare the results to traditional on-premises compute clusters. Our use case is atomistic …
How do the size, charge and shape of nanoparticles affect amyloid β aggregation on brain lipid bilayer?
Y Kim, JH Park, H Lee, JM Nam - Scientific reports, 2016 - nature.com
Here, we studied the effect of the size, shape and surface charge of Au nanoparticles
(AuNPs) on amyloid beta (Aβ) aggregation on a total brain lipid-based supported lipid …
(AuNPs) on amyloid beta (Aβ) aggregation on a total brain lipid-based supported lipid …
Advances in the simulation of protein aggregation at the atomistic scale
Protein aggregation into highly structured amyloid fibrils is associated with various diseases
including Alzheimer's disease, Parkinson's disease, and type II diabetes. Amyloids can also …
including Alzheimer's disease, Parkinson's disease, and type II diabetes. Amyloids can also …
Formation and propagation of tau oligomeric seeds
JE Gerson, R Kayed - Frontiers in neurology, 2013 - frontiersin.org
Tau misfolding and aggregation leads to the formation of neurofibrillary tangles (NFTs),
which have long been considered one of the main pathological hallmarks for numerous …
which have long been considered one of the main pathological hallmarks for numerous …
Understanding amyloid fibril nucleation and Aβ oligomer/drug interactions from computer simulations
P Nguyen, P Derreumaux - Accounts of chemical research, 2014 - ACS Publications
Evolution has fine-tuned proteins to accomplish a variety of tasks. Yet, with aging, some
proteins assemble into harmful amyloid aggregates associated with neurodegenerative …
proteins assemble into harmful amyloid aggregates associated with neurodegenerative …
Amyloid self‐assembly of hIAPP8‐20 via the accumulation of helical oligomers, α‐helix to β‐sheet transition, and formation of β‐barrel intermediates
The self‐assembly of human islet amyloid polypeptide (hIAPP) into β‐sheet‐rich nanofibrils
is associated with the pathogeny of type 2 diabetes. Soluble hIAPP is intrinsically disordered …
is associated with the pathogeny of type 2 diabetes. Soluble hIAPP is intrinsically disordered …
On the applicability of force fields to study the aggregation of amyloidogenic peptides using molecular dynamics simulations
Molecular dynamics simulations play an essential role in understanding biomolecular
processes such as protein aggregation at temporal and spatial resolutions which are not …
processes such as protein aggregation at temporal and spatial resolutions which are not …
Phosphorylation drives a dynamic switch in serine/arginine-rich proteins
Summary Serine/arginine-rich (SR) proteins are important players in RNA metabolism and
are extensively phosphorylated at serine residues in RS repeats. Here, we show that …
are extensively phosphorylated at serine residues in RS repeats. Here, we show that …