Enhanced sampling methods for molecular dynamics simulations

J Hénin, T Lelièvre, MR Shirts, O Valsson… - arXiv preprint arXiv …, 2022 - arxiv.org
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …

Proteostasis of islet amyloid polypeptide: a molecular perspective of risk factors and protective strategies for type II diabetes

D Milardi, E Gazit, SE Radford, Y Xu… - Chemical …, 2021 - ACS Publications
The possible link between hIAPP accumulation and β-cell death in diabetic patients has
inspired numerous studies focusing on amyloid structures and aggregation pathways of this …

Hierarchical materials from high information content macromolecular building blocks: construction, dynamic interventions, and prediction

L Shao, J Ma, JL Prelesnik, Y Zhou, M Nguyen… - Chemical …, 2022 - ACS Publications
Hierarchical materials that exhibit order over multiple length scales are ubiquitous in nature.
Because hierarchy gives rise to unique properties and functions, many have sought …

[HTML][HTML] Enhancing geometric representations for molecules with equivariant vector-scalar interactive message passing

Y Wang, T Wang, S Li, X He, M Li, Z Wang… - Nature …, 2024 - nature.com
Geometric deep learning has been revolutionizing the molecular modeling field. Despite the
state-of-the-art neural network models are approaching ab initio accuracy for molecular …

Amyloid aggregation simulations: challenges, advances and perspectives

B Strodel - Current opinion in structural biology, 2021 - Elsevier
In amyloid aggregation diseases soluble proteins coalesce into a wide array of undesirable
structures, ranging through oligomers and prefibrillar assemblies to highly ordered amyloid …

Revolutionizing peptide‐based drug discovery: Advances in the post‐AlphaFold era

L Chang, A Mondal, B Singh… - Wiley …, 2024 - Wiley Online Library
Peptide‐based drugs offer high specificity, potency, and selectivity. However, their inherent
flexibility and differences in conformational preferences between their free and bound states …

Computational methods for exploring protein conformations

JR Allison - Biochemical Society Transactions, 2020 - portlandpress.com
Proteins are dynamic molecules that can transition between a potentially wide range of
structures comprising their conformational ensemble. The nature of these conformations and …

[HTML][HTML] An investigation into the potential action of polyphenols against human Islet Amyloid Polypeptide aggregation in type 2 diabetes

A Mahboob, DKL Senevirathne, P Paul, F Nabi… - International Journal of …, 2023 - Elsevier
Abstract Type 2 diabetes (T2D), a chronic metabolic disease characterized by
hyperglycemia, results in significant disease burden and financial costs globally. Whilst the …

Biomaterial‐interrelated bacterial sweeper: simplified self‐assembled octapeptides with double‐layered Trp zipper induces membrane destabilization and bacterial …

Y Fang, Y Zhu, L Li, Z Lai, N Dong, A Shan - Small Methods, 2021 - Wiley Online Library
Abstract Treatment of microbial‐associated infections continues to be hampered by impaired
antibacterial efficiency and the variability in nanomedicines. Herein, an octapeptide library …

[HTML][HTML] Enhanced sampling without borders: on global biasing functions and how to reweight them

AS Kamenik, SM Linker, S Riniker - Physical Chemistry Chemical …, 2022 - pubs.rsc.org
Molecular dynamics (MD) simulations are a powerful tool to follow the time evolution of
biomolecular motions in atomistic resolution. However, the high computational demand of …