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Regularizing binding energy distributions and thermodynamics of hydration. Application to water modeled with classical and ab initio simulations
potential distribution theorem hydration free energy hybrid Monte Carlo vapor-liquid equilibrium
2011/8/5
Abstract: The high-energy tail of the distribution of solute-solvent interaction energies is poorly characterized for condensed systems, but this tail region is of principal interest in determining th...
The forward and backward stepping processes of kinesin are gated by ATP binding
kinesin optical trapping nanometry single molecule 8-nm steps mechanochemical coupling
2010/12/2
The kinesin motor converts the chemical energy from ATP turnover into mechanical work, which produces successive 8-nm steps in the forward and backward direction along a microtubule. A key problem for...
The role of charged surface residues in the binding ability of small hubs in protein-protein interaction networks
protein-protein interaction networks hubs electrostatic potential multipole expansion surface charge
2010/12/2
Hubs are highly connected proteins in a protein-protein interaction network. Previous work has implicated disordered domains and high surface charge as the properties significant in the ability of hub...
Generation of a flexible loop structural ensemble and its application to induced-fit structural changes following ligand binding
docking simulation flexible loop modeling force-biased multicanonical molecular dynamics induced-fit structural ensemble
2010/12/2
Molecular recognition is often mediated by flexible loops that have widely fluctuating structures and are sometimes disordered, but that form particular complex structures following ligand binding. In...