Integration of molecular docking analysis and molecular dynamics simulations for studying food proteins and bioactive peptides

A Vidal-Limon, JE Aguilar-Toalá… - Journal of Agricultural …, 2022 - ACS Publications
In silico tools, such as molecular docking, are widely applied to study interactions and
binding affinity of biological activity of proteins and peptides. However, restricted sampling of …

Perspectives on external electric fields in molecular simulation: progress, prospects and challenges

NJ English, CJ Waldron - Physical Chemistry Chemical Physics, 2015 - pubs.rsc.org
In this review, the application of a wide variety of external electric fields in molecular
simulation shall be discussed, including time-varying and electromagnetic, as well as the …

Molecular simulation of water in carbon nanotubes

A Alexiadis, S Kassinos - Chemical reviews, 2008 - ACS Publications
According to Monthioux and Kuznetsov, 1 the first mention of carbon filaments was reported
in 18892 in a patent proposing the use of such filaments in light bulbs (interestingly enough …

Modeling and simulation of ion channels

C Maffeo, S Bhattacharya, J Yoo, D Wells… - Chemical …, 2012 - ACS Publications
Transport of ions through pores in membranes is a process of fundamental importance to
cell biology. In living organisms, such transport is facilitated by ion channels that utilize the …

Computational investigation of DNA detection using graphene nanopores

C Sathe, X Zou, JP Leburton, K Schulten - ACS nano, 2011 - ACS Publications
Nanopore-based single-molecule detection and analysis have been pursued intensively
over the past decade. One of the most promising applications in this regard is DNA …

Theoretical approaches to graphene and graphene-based materials

T Zhang, Q Xue, S Zhang, M Dong - Nano Today, 2012 - Elsevier
Graphene with its peculiar and exceptional properties has been widely used in the
preparation of next generation functional nanocomposites. However, future development of …

The multiple faces of self-assembled lipidic systems

G Tresset - PMC biophysics, 2009 - Springer
Lipids, the building blocks of cells, common to every living organisms, have the propensity to
self-assemble into well-defined structures over short and long-range spatial scales. The …

On the spontaneous encapsulation of proteins in carbon nanotubes

Y Kang, YC Liu, Q Wang, JW Shen, T Wu, WJ Guan - Biomaterials, 2009 - Elsevier
Biomolecules–carbon nanotube (CNT) interactions are of great importance in CNT-based
drug delivery systems and biomedical devices. In this study, a spontaneous encapsulation of …

Disassembly of nanodiscs with cholate

AY Shih, PL Freddolino, SG Sligar, K Schulten - Nano letters, 2007 - ACS Publications
Nanodiscs are protein− lipid particles that furnish a nanometer-sized membrane
environment for the investigation of membrane proteins. Nanodiscs assemble …

Boron nitride nanotube as an antimicrobial peptide carrier: a theoretical insight

M Zarghami Dehaghani, B Bagheri… - International Journal …, 2021 - Taylor & Francis
Introduction Nanotube-based drug delivery systems have received considerable attention
because of their large internal volume to encapsulate the drug and the ability to penetrate …