Amyloid oligomers: A joint experimental/computational perspective on Alzheimer's disease, Parkinson's disease, type II diabetes, and amyotrophic lateral sclerosis

PH Nguyen, A Ramamoorthy, BR Sahoo… - Chemical …, 2021 - ACS Publications
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting
either the central nervous system or a variety of peripheral tissues. Structural and dynamic …

Large-scale computations in chemistry: a bird's eye view of a vibrant field

AV Akimov, OV Prezhdo - Chemical reviews, 2015 - ACS Publications
1.1. The Meaning of “Large Scale” In general, the term “large scale” can have one of the
following five meanings in computational chemistry:(1) large size: power-law and …

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

Z Miao, RW Adamiak, M Antczak, MJ Boniecki… - Rna, 2020 - rnajournal.cshlp.org
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of
RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are …

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Z Miao, RW Adamiak, M Antczak, RT Batey, AJ Becka… - Rna, 2017 - rnajournal.cshlp.org
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here
a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch …

Automated minimization of steric clashes in protein structures

S Ramachandran, P Kota, F Ding… - Proteins: Structure …, 2011 - Wiley Online Library
Molecular modeling of proteins including homology modeling, structure determination, and
knowledge-based protein design requires tools to evaluate and refine three-dimensional …

Controlling allosteric networks in proteins

NV Dokholyan - Chemical reviews, 2016 - ACS Publications
Allosteric transition, defined as conformational changes induced by ligand binding, is one of
the fundamental properties of proteins. Allostery has been observed and characterized in …

[HTML][HTML] Ab initio folding of proteins with all-atom discrete molecular dynamics

F Ding, D Tsao, H Nie, NV Dokholyan - Structure, 2008 - cell.com
Discrete molecular dynamics (DMD) is a rapid sampling method used in protein folding and
aggregation studies. Until now, DMD was used to perform simulations of simplified protein …

Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet

E Shakhnovich - Chemical reviews, 2006 - ACS Publications
As was noted in our recent review, 1 the protein folding field underwent a cyclic
development. Initially, protein folding was viewed as a strictly experimental field belonging to …

Graphene quantum dots against human IAPP aggregation and toxicity in vivo

M Wang, Y Sun, X Cao, G Peng, I Javed, A Kakinen… - Nanoscale, 2018 - pubs.rsc.org
The development of biocompatible nanomaterials has become a new frontier in the
detection, treatment and prevention of human amyloid diseases. Here we demonstrated the …

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 …