Steered molecular dynamics simulation in rational drug design

PC Do, EH Lee, L Le - Journal of Chemical Information and …, 2018 - ACS Publications
Conventional de novo drug design is time consuming, laborious, and resource intensive. In
recent years, emerging in silico approaches have been proven to be critical to accelerate the …

Next generation methods for single-molecule force spectroscopy on polyproteins and receptor-ligand complexes

B Yang, Z Liu, H Liu, MA Nash - Frontiers in Molecular Biosciences, 2020 - frontiersin.org
Single-molecule force spectroscopy with the atomic force microscope provides molecular
level insights into protein function, allowing researchers to reconstruct energy landscapes …

From molecular mechanochemistry to stress-responsive materials

AL Black, JM Lenhardt, SL Craig - Journal of Materials Chemistry, 2011 - pubs.rsc.org
Current activity in, and future prospects for, the incorporation of mechanochemically active
functional groups (“mechanophores”) into polymers is reviewed. This area of research is …

Thiol-based, site-specific and covalent immobilization of biomolecules for single-molecule experiments

JL Zimmermann, T Nicolaus, G Neuert, K Blank - Nature protocols, 2010 - nature.com
The success of single-molecule (SM) experiments critically depends on the functional
immobilization of the biomolecule (s) to be studied. With the continuing trend of combining …

Grading the commercial optical biosensor literature—Class of 2008:'The Mighty Binders'

RL Rich, DG Myszka - Journal of Molecular Recognition: An …, 2010 - Wiley Online Library
Optical biosensor technology continues to be the method of choice for label‐free, real‐time
interaction analysis. But when it comes to improving the quality of the biosensor literature …

Molecular dynamics simulation study of xyloglucan adsorption on cellulose surfaces: effects of surface hydrophobicity and side-chain variation

Z Zhao, VH Crespi, JD Kubicki, DJ Cosgrove, L Zhong - Cellulose, 2014 - Springer
The effect of surface hydrophobicity and side-chain variation on xyloglucan adsorption onto
cellulose microfibrils (CMF) is investigated via molecular dynamics simulations. A molecular …

Lagrangian descriptors of thermalized transition states on time-varying energy surfaces

GT Craven, R Hernandez - Physical review letters, 2015 - APS
Thermalized chemical reactions driven under dynamical load are characteristic of activated
dynamics for arbitrary nonautonomous systems. Recent generalizations of transition state …

Force spectroscopy 101: how to design, perform, and analyze an AFM-based single molecule force spectroscopy experiment

A Noy - Current opinion in chemical biology, 2011 - Elsevier
Single molecule force spectroscopy presents a deceptively simple approach to probing
interaction between molecules and molecular assemblies on the nanoscale by measuring …

Multidimensional minimum-work control of a 2D Ising model

MD Louwerse, DA Sivak - The Journal of Chemical Physics, 2022 - pubs.aip.org
A system's configurational state can be manipulated using dynamic variation of control
parameters, such as temperature, pressure, or magnetic field; for finite-duration driving …

Deconstructing field-induced ketene isomerization through Lagrangian descriptors

GT Craven, R Hernandez - Physical Chemistry Chemical Physics, 2016 - pubs.rsc.org
The time-dependent geometrical separatrices governing state transitions in field-induced
ketene isomerization are constructed using the method of Lagrangian descriptors. We obtain …