Simulations of the unliganded human hemoglobin tetramer, which for the first time yield a thermodynamically stable system, cast doubts on the use of standard solvent box sizes for molecular dynamics studies of biological macromolecules.
The use of adequate statistics is demonstrated to be an essential prerequisite to derive conclusions on thermodynamics and kinetics from molecular simulations.
We are writing to respond to the comment by Gapsys and de Groot, 2019 on our article about molecular dynamics simulations of human hemoglobin (El Hage et al., 2018).
A simulation study is used to demonstrate how mistakes in identifying the experimental unit and the unit of analysis can lead to incorrect analyses and inappropriate inferences when reporting research studies.
Ded1p and eIF4A, two RNA helicases that function in eukaryotic translation initiation, interact physically with each other and with the scaffolding protein eIF4G.
Computational modeling of the brain’s navigation system reveals that place cells can drive the formation of hexagonal patterns experimentally observed in grid cells activity.
The transcription and splicing factor T-box3 is present in primary cilia, regulates multiple aspects of limb development, and interacts with members of the protein complex required for the stability and processing of the Gli3 transcription factor.
Multimegadalton intraflagellar transport (IFT) trains assemble by sequential recruitment of IFT subcomplexes from the cell body to the ciliary basal bodies and tubulin, the main IFT cargo, is loaded briefly before trains depart.
