Free energy methods for the description of molecular processes

C Chipot - Annual Review of Biophysics, 2023 - annualreviews.org
Efforts to combine theory and experiment to advance our knowledge of molecular processes
relevant to biophysics have been considerably enhanced by the contribution of statistical …

The effects of vitamin B in depression

K Mikkelsen, L Stojanovska… - Current medicinal …, 2016 - ingentaconnect.com
Vitamins are dietary components which are necessary for life. They play a major role in
health and their deficiency may be linked to symptoms of psychiatric disorders. B vitamins …

Standard binding free energies from computer simulations: What is the best strategy?

JC Gumbart, B Roux, C Chipot - Journal of chemical theory and …, 2013 - ACS Publications
Accurate prediction of standard binding free energies describing protein–ligand association
remains a daunting computational endeavor. This challenge is rooted to a large extent in the …

Integrin and cadherin clusters: A robust way to organize adhesions for cell mechanics

R Changede, M Sheetz - BioEssays, 2017 - Wiley Online Library
Recent studies at the nanometer scale have revealed that relatively uniform clusters of
adhesion proteins (50–100 nm) constitute the modular units of cell adhesion sites in both …

[HTML][HTML] Physics in nanomedicine: Phenomena governing the in vivo performance of nanoparticles

LA Lane - Applied Physics Reviews, 2020 - pubs.aip.org
Nanomedicine aims to increase the effectiveness of therapeutic and diagnostic agents by
exploiting unique properties that arise when operating at the nanoscale. Despite the recent …

Integrin-generated forces lead to streptavidin-biotin unbinding in cellular adhesions

C Jurchenko, Y Chang, Y Narui, Y Zhang, KS Salaita - Biophysical journal, 2014 - cell.com
The interplay between chemical and mechanical signals plays an important role in cell
biology, and integrin receptors are the primary molecules involved in sensing and …

Experimental and theoretical investigations in stimuli responsive dendrimer-based assemblies

MR Molla, P Rangadurai, GM Pavan, S Thayumanavan - Nanoscale, 2015 - pubs.rsc.org
Stimuli-responsive macromolecular assemblies are of great interest in drug delivery
applications, as it holds the promise to keep the drug molecules sequestered under one set …

Detailed characterization of the solution kinetics and thermodynamics of biotin, biocytin and HABA binding to avidin and streptavidin

RF Delgadillo, TC Mueser, K Zaleta-Rivera, KA Carnes… - PloS one, 2019 - journals.plos.org
The high affinity (KD~ 10− 15 M) of biotin for avidin and streptavidin is the essential
component in a multitude of bioassays with many experiments using biotin modifications to …

Binding affinity estimation from restrained umbrella sampling simulations

V Govind Kumar, A Polasa, S Agrawal… - Nature Computational …, 2023 - nature.com
The protein–ligand binding affinity quantifies the binding strength between a protein and its
ligand. Computer modeling and simulations can be used to estimate the binding affinity or …

Calculation of protein–ligand binding affinities based on a fragment quantum mechanical method

J Liu, X Wang, JZH Zhang, X He - Rsc Advances, 2015 - pubs.rsc.org
An electrostatically embedded generalized molecular fractionation with conjugate caps (EE-
GMFCC) method (J. Phys. Chem. A, 2013, 117, 7149) has been successfully used for …