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CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to(More)
Protein-lipid interaction and bilayer regulation of membrane protein functions are largely controlled by the hydrophobic match between the transmembrane (TM) domain of membrane proteins and the surrounding lipid bilayer. To systematically characterize responses of a TM helix and lipid adaptations to a hydrophobic mismatch, we have performed a total of(More)
Molecular dynamics simulations of membrane proteins have provided deeper insights into their functions and interactions with surrounding environments at the atomic level. However, compared to solvation of globular proteins, building a realistic protein/membrane complex is still challenging and requires considerable experience with simulation software.(More)
Analytical compact-form models for the signal transients and crosstalk noise of inductive-effect-prominent multicoupled lines are developed. Capacitive and inductive coupling effects are investigated and formulated in terms of the effective single-transmission-line model and effective transmission line parameters for fundamental switching modes. Arbitrary(More)
<i>Background:</i> Finding relevant articles from PubMed is challenging because it is hard to express the user's specific intention in the given query interface, and a keyword query typically retrieves a large number of results. Researchers have applied machine learning techniques to find relevant articles by ranking the articles according to the learned(More)
Because of the openness and anonymity of peer-to-peer (P2P) networks, P2P participants can easily spread inauthentic resources such as viruses or worms throughout Internet. Besides, the deployment of such inauthentic resources in P2P networks has a chance of posing serious problems, thus, the trust on P2P participants needs to be carefully considered. A(More)
A method of window exchange umbrella sampling molecular dynamics simulation is employed for transmembrane helix assembly. An analytical expression for the average acceptance probability between neighboring windows is derived and combined with the first passage time optimization method to predetermine a parameter set in an optimal range. With the parameter(More)