pH-induced conformational switching is essential for functioning of diphtheria toxin, which
undergoes a membrane insertion/translocation transition triggered by endosomal acidification …

Sugars are essential sources of energy and carbon and also function as key signalling
molecules in plants. Sugar transport proteins (STP) are proton-coupled symporters responsible …

Identification of modules in molecular networks is at the core of many current analysis
methods in biomedical research. However, how well different approaches identify disease-…

… Jose C. Flores-Canales and Maria Kurnikova performed and analyzed the MD simulations.
Mauricio Vargas-Uribe, Chiranjib Ghatak and Alexey S. Ladokhin wrote the manuscript. …

For protein structure modeling in the CASP12 experiment, we have developed a new
protocol based on our previous CASP11 approach. The global optimization method of …

Accelerated molecular dynamics (aMD) is a promising sampling method to generate an
ensemble of conformations and to explore the free energy landscape of proteins in explicit …

Independent force field validation is an essential practice to keep track of developments and
for performing meaningful Molecular Dynamics simulations. In this work, atomistic force …

Diphtheria toxin translocation (T) domain inserts in lipid bilayers upon acidification of the
environment. Computational and experimental studies have suggested that low pH triggers a …

Diphtheria toxin translocation (T) domain undergoes conformational changes in acidic
solution and associates with the lipid membranes, followed by refolding and transmembrane …

This work measures baseline sampling characteristics that highlight fundamental differences
between sampling methods for assembly driven by short-ranged pair potentials. Such …