Molecular dynamics simulations and novel drug discovery
X Liu, D Shi, S Zhou, H Liu, H Liu… - Expert opinion on drug …, 2018 - Taylor & Francis
Introduction: Molecular dynamics (MD) simulations can provide not only plentiful dynamical
structural information on biomacromolecules but also a wealth of energetic information …
structural information on biomacromolecules but also a wealth of energetic information …
Amyloid β protein and Alzheimer's disease: When computer simulations complement experimental studies
J Nasica-Labouze, PH Nguyen, F Sterpone… - Chemical …, 2015 - ACS Publications
Alzheimer's disease (AD) challenges our society with an annual estimated cost of $1.08
trillion in the United States alone by 2050. 1 AD is a progressive irreversible neurological …
trillion in the United States alone by 2050. 1 AD is a progressive irreversible neurological …
Simulation studies of amyloidogenic polypeptides and their aggregates
IM Ilie, A Caflisch - Chemical reviews, 2019 - ACS Publications
Amyloids, fibrillar assembly of (poly) peptide chains, are associated with neurodegenerative
illnesses such as Alzheimer's and Parkinson's diseases, for which there are no cures. The …
illnesses such as Alzheimer's and Parkinson's diseases, for which there are no cures. The …
Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics
Although it is known that RNA undergoes liquid–liquid phase separation, the interplay
between the molecular driving forces and the emergent features of the condensates, such as …
between the molecular driving forces and the emergent features of the condensates, such as …
Role of water in protein aggregation and amyloid polymorphism
A variety of neurodegenerative diseases are associated with amyloid plaques, which begin
as soluble protein oligomers but develop into amyloid fibrils. Our incomplete understanding …
as soluble protein oligomers but develop into amyloid fibrils. Our incomplete understanding …
Different force fields give rise to different amyloid aggregation pathways in molecular dynamics simulations
S Samantray, F Yin, B Kav… - Journal of chemical …, 2020 - ACS Publications
The progress toward understanding the molecular basis of Alzheimers's disease is strongly
connected to elucidating the early aggregation events of the amyloid-β (Aβ) peptide …
connected to elucidating the early aggregation events of the amyloid-β (Aβ) peptide …
Polymorphism in Alzheimer Aβ amyloid organization reflects conformational selection in a rugged energy landscape
Amyloids can have normal biological functions. 1r3 However, amyloidogenic proteins can
also form unwanted oligomeric or polymeric aggregates when disturbed from their native …
also form unwanted oligomeric or polymeric aggregates when disturbed from their native …
Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of Aβ16–22 Dimer
We investigated the effects of 17 widely used atomistic molecular mechanics force fields
(MMFFs) on the structures and kinetics of amyloid peptide assembly. To this end, we …
(MMFFs) on the structures and kinetics of amyloid peptide assembly. To this end, we …
Toward a molecular theory of early and late events in monomer to amyloid fibril formation
JE Straub, D Thirumalai - Annual review of physical chemistry, 2011 - annualreviews.org
Quantitative understanding of the kinetics of fibril formation and the molecular mechanism of
transition from monomers to fibrils is needed to obtain insights into the growth of amyloid …
transition from monomers to fibrils is needed to obtain insights into the growth of amyloid …
High-resolution probing of early events in amyloid-β aggregation related to Alzheimer's disease
In Alzheimer's disease (AD), soluble oligomers of amyloid-β (Aβ) are emerging as a crucial
entity in driving disease progression as compared to insoluble amyloid deposits. The lacuna …
entity in driving disease progression as compared to insoluble amyloid deposits. The lacuna …